Starting phenix.real_space_refine on Mon Aug 25 11:02:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmh_61602/08_2025/9jmh_61602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmh_61602/08_2025/9jmh_61602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jmh_61602/08_2025/9jmh_61602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmh_61602/08_2025/9jmh_61602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmh_61602/08_2025/9jmh_61602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmh_61602/08_2025/9jmh_61602.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.238 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 144 5.16 5 C 17360 2.51 5 N 4474 2.21 5 O 5474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27452 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8778 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1066} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8784 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 54, 'TRANS': 1066} Chain breaks: 10 Chain: "C" Number of atoms: 8784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8784 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 54, 'TRANS': 1066} Chain breaks: 10 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 222 Unusual residues: {'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.65, per 1000 atoms: 0.21 Number of scatterers: 27452 At special positions: 0 Unit cell: (151.8, 145.2, 161.04, 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 144 16.00 O 5474 8.00 N 4474 7.00 C 17360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 245 " distance=2.05 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS B1051 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 584 " distance=2.04 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 653 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.06 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 917 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS C 437 " distance=2.04 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 222 " distance=2.01 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 245 " distance=2.04 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS C1051 " distance=2.03 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 653 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 678 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 809 " distance=2.04 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS B 917 " distance=2.03 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 245 " distance=2.06 Simple disulfide: pdb=" SG CYS C 347 " - pdb=" SG CYS C 357 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 445 " - pdb=" SG CYS C 584 " distance=2.02 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS C 531 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 653 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 678 " - pdb=" SG CYS C 711 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.06 Simple disulfide: pdb=" SG CYS C 798 " - pdb=" SG CYS C 820 " distance=2.03 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 809 " distance=2.04 Simple disulfide: pdb=" SG CYS C 904 " - pdb=" SG CYS C 917 " distance=2.03 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1402 " - " ASN A 66 " " NAG A1403 " - " ASN A 111 " " NAG A1404 " - " ASN A 163 " " NAG A1405 " - " ASN A 167 " " NAG A1406 " - " ASN A 241 " " NAG A1407 " - " ASN A 252 " " NAG A1408 " - " ASN A 591 " " NAG A1409 " - " ASN A 618 " " NAG A1410 " - " ASN A 717 " " NAG A1411 " - " ASN A 755 " " NAG A1412 " - " ASN A 777 " " NAG A1413 " - " ASN A 862 " " NAG A1414 " - " ASN A1207 " " NAG B1401 " - " ASN B 66 " " NAG B1402 " - " ASN B 163 " " NAG B1403 " - " ASN B 167 " " NAG B1404 " - " ASN B 241 " " NAG B1405 " - " ASN B 252 " " NAG B1406 " - " ASN B 591 " " NAG B1407 " - " ASN B 618 " " NAG B1408 " - " ASN B 717 " " NAG B1409 " - " ASN B 755 " " NAG B1410 " - " ASN B 777 " " NAG B1411 " - " ASN B 862 " " NAG B1412 " - " ASN B1207 " " NAG C1401 " - " ASN C 66 " " NAG C1402 " - " ASN C 111 " " NAG C1403 " - " ASN C 163 " " NAG C1404 " - " ASN C 167 " " NAG C1405 " - " ASN C 241 " " NAG C1406 " - " ASN C 252 " " NAG C1407 " - " ASN C 591 " " NAG C1408 " - " ASN C 618 " " NAG C1409 " - " ASN C 717 " " NAG C1410 " - " ASN C 755 " " NAG C1411 " - " ASN C 777 " " NAG C1412 " - " ASN C 862 " " NAG C1413 " - " ASN C1207 " " NAG D 1 " - " ASN A 114 " " NAG E 1 " - " ASN A 174 " " NAG F 1 " - " ASN A 230 " " NAG G 1 " - " ASN A 132 " " NAG H 1 " - " ASN A 418 " " NAG I 1 " - " ASN B 111 " " NAG J 1 " - " ASN B 114 " " NAG K 1 " - " ASN B 132 " " NAG L 1 " - " ASN B 174 " " NAG M 1 " - " ASN B 230 " " NAG N 1 " - " ASN B 418 " " NAG O 1 " - " ASN C 114 " " NAG P 1 " - " ASN C 132 " " NAG Q 1 " - " ASN C 174 " " NAG R 1 " - " ASN C 230 " " NAG S 1 " - " ASN C 418 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 54 sheets defined 26.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.780A pdb=" N GLN A 41 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.512A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.561A pdb=" N SER A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.919A pdb=" N VAL A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.642A pdb=" N GLU A 810 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 812 " --> pdb=" O LYS A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 845 removed outlier: 4.379A pdb=" N CYS A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 821 " --> pdb=" O GLY A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.306A pdb=" N VAL A 921 " --> pdb=" O CYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 946 removed outlier: 3.518A pdb=" N GLY A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 946 " --> pdb=" O SER A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 985 through 998 Processing helix chain 'A' and resid 1008 through 1031 removed outlier: 4.064A pdb=" N ASN A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A1022 " --> pdb=" O VAL A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1042 through 1050 Processing helix chain 'A' and resid 1051 through 1098 removed outlier: 3.799A pdb=" N GLU A1056 " --> pdb=" O PRO A1052 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA A1057 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1062 " --> pdb=" O GLN A1058 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1217 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.581A pdb=" N ALA B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.668A pdb=" N PHE B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 457 through 461 Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 677 through 682 removed outlier: 3.684A pdb=" N VAL B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 817 through 845 removed outlier: 4.373A pdb=" N ALA B 821 " --> pdb=" O GLY B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 890 Processing helix chain 'B' and resid 899 through 907 removed outlier: 4.020A pdb=" N GLN B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 4.609A pdb=" N VAL B 921 " --> pdb=" O CYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 946 Processing helix chain 'B' and resid 963 through 975 Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 3.612A pdb=" N MET B1000 " --> pdb=" O ALA B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1003 No H-bonds generated for 'chain 'B' and resid 1001 through 1003' Processing helix chain 'B' and resid 1008 through 1031 removed outlier: 3.754A pdb=" N LEU B1025 " --> pdb=" O ASN B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1042 through 1050 Processing helix chain 'B' and resid 1051 through 1098 removed outlier: 4.555A pdb=" N GLU B1056 " --> pdb=" O PRO B1052 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA B1057 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B1058 " --> pdb=" O GLU B1054 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B1061 " --> pdb=" O ALA B1057 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B1089 " --> pdb=" O ALA B1085 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B1090 " --> pdb=" O ARG B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1217 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.925A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 41' Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 230 through 239 removed outlier: 3.558A pdb=" N HIS C 238 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 393 through 399 removed outlier: 4.155A pdb=" N GLY C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 457 through 465 removed outlier: 5.143A pdb=" N SER C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 464 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 Processing helix chain 'C' and resid 531 through 536 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 677 through 682 removed outlier: 3.766A pdb=" N VAL C 681 " --> pdb=" O ALA C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 804 Processing helix chain 'C' and resid 806 through 814 Processing helix chain 'C' and resid 816 through 845 removed outlier: 4.100A pdb=" N CYS C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 821 " --> pdb=" O GLY C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 890 Processing helix chain 'C' and resid 899 through 907 removed outlier: 3.822A pdb=" N GLN C 907 " --> pdb=" O GLU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 923 Processing helix chain 'C' and resid 932 through 946 Processing helix chain 'C' and resid 963 through 975 removed outlier: 3.667A pdb=" N ILE C 975 " --> pdb=" O ARG C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 985 through 1001 removed outlier: 4.151A pdb=" N GLN C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'C' and resid 1008 through 1031 Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1042 through 1050 Processing helix chain 'C' and resid 1054 through 1099 removed outlier: 3.658A pdb=" N GLN C1058 " --> pdb=" O GLU C1054 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C1061 " --> pdb=" O ALA C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1213 through 1217 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.500A pdb=" N SER A 63 " --> pdb=" O TYR C 631 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 630 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR C 638 " --> pdb=" O VAL C 650 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR C 647 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 617 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 76 removed outlier: 3.532A pdb=" N GLY A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 271 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A 291 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 273 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.208A pdb=" N ARG A 343 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 removed outlier: 4.068A pdb=" N ASN A 117 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 301 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA A 159 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N HIS A 175 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE A 161 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU A 173 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N TYR A 172 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN A 174 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 195 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 192 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 247 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 194 " --> pdb=" O CYS A 245 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS A 245 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 196 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR A 243 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.578A pdb=" N ARG A 146 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 214 through 216 removed outlier: 6.392A pdb=" N ILE A 214 " --> pdb=" O SER A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 371 removed outlier: 3.556A pdb=" N VAL A 371 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 658 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 381 through 384 Processing sheet with id=AB1, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.506A pdb=" N SER A 448 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 491 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 428 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AB3, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.529A pdb=" N GLN A 519 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 556 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS A 510 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 554 " --> pdb=" O CYS A 510 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 553 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.363A pdb=" N VAL A 630 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 722 removed outlier: 6.673A pdb=" N VAL A 716 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N VAL A 753 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N SER A 718 " --> pdb=" O VAL A 753 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 760 through 761 removed outlier: 5.608A pdb=" N HIS A 760 " --> pdb=" O THR B 850 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1113 through 1122 removed outlier: 5.857A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE A1164 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1113 through 1122 removed outlier: 5.857A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY A1125 " --> pdb=" O GLN A 788 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN A 788 " --> pdb=" O GLY A1125 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A1127 " --> pdb=" O TYR A 786 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR A 786 " --> pdb=" O TYR A1127 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A1129 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN A 784 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1131 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 782 " --> pdb=" O VAL A1131 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR A1133 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE A 780 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE A 778 " --> pdb=" O PRO A1135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A1137 " --> pdb=" O THR A 776 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AC1, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AC2, first strand: chain 'A' and resid 959 through 960 removed outlier: 6.383A pdb=" N PHE C 778 " --> pdb=" O PRO C1135 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE C 780 " --> pdb=" O TYR C1133 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR C1133 " --> pdb=" O PHE C 780 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 782 " --> pdb=" O VAL C1131 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C1131 " --> pdb=" O ILE C 782 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN C 784 " --> pdb=" O PHE C1129 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE C1129 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 786 " --> pdb=" O TYR C1127 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR C1127 " --> pdb=" O TYR C 786 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN C 788 " --> pdb=" O GLY C1125 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C1125 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY C1125 " --> pdb=" O ASN C1121 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN C1121 " --> pdb=" O GLY C1125 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR C1127 " --> pdb=" O VAL C1119 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C1119 " --> pdb=" O TYR C1127 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C1129 " --> pdb=" O SER C1117 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C1117 " --> pdb=" O PHE C1129 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C1131 " --> pdb=" O ILE C1115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 959 through 960 removed outlier: 6.383A pdb=" N PHE C 778 " --> pdb=" O PRO C1135 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE C 780 " --> pdb=" O TYR C1133 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR C1133 " --> pdb=" O PHE C 780 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 782 " --> pdb=" O VAL C1131 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C1131 " --> pdb=" O ILE C 782 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN C 784 " --> pdb=" O PHE C1129 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE C1129 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 786 " --> pdb=" O TYR C1127 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR C1127 " --> pdb=" O TYR C 786 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN C 788 " --> pdb=" O GLY C1125 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C1125 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C1164 " --> pdb=" O ALA C1144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1196 through 1199 removed outlier: 4.011A pdb=" N CYS A1156 " --> pdb=" O VAL A1199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.189A pdb=" N ARG B 343 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.076A pdb=" N ALA B 320 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY B 128 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 290 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER B 275 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 288 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.073A pdb=" N ASN B 117 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA B 154 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA B 159 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N HIS B 175 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE B 161 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 173 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N TYR B 172 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN B 174 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 195 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 192 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 247 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 194 " --> pdb=" O CYS B 245 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 245 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 196 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR B 243 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AD1, first strand: chain 'B' and resid 214 through 216 removed outlier: 6.377A pdb=" N ILE B 214 " --> pdb=" O SER B 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 367 through 371 removed outlier: 4.742A pdb=" N LEU B 658 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 668 " --> pdb=" O ASP B 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 381 through 384 removed outlier: 6.707A pdb=" N PHE B 382 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 408 through 412 removed outlier: 3.778A pdb=" N LEU B 566 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR B 491 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B 428 " --> pdb=" O THR B 491 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 416 through 417 Processing sheet with id=AD6, first strand: chain 'B' and resid 517 through 520 removed outlier: 3.792A pdb=" N SER B 514 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASN B 505 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA B 560 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU B 507 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN B 558 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 647 through 648 removed outlier: 6.177A pdb=" N VAL B 630 " --> pdb=" O THR B 638 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 716 through 722 removed outlier: 6.795A pdb=" N VAL B 716 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL B 753 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N SER B 718 " --> pdb=" O VAL B 753 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 760 through 762 removed outlier: 5.693A pdb=" N HIS B 760 " --> pdb=" O THR C 850 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1113 through 1121 removed outlier: 7.115A pdb=" N VAL B1131 " --> pdb=" O ILE B1115 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER B1117 " --> pdb=" O PHE B1129 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B1129 " --> pdb=" O SER B1117 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B1119 " --> pdb=" O TYR B1127 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B1127 " --> pdb=" O VAL B1119 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN B1121 " --> pdb=" O GLY B1125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY B1125 " --> pdb=" O ASN B1121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B1164 " --> pdb=" O ALA B1144 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B1163 " --> pdb=" O THR B1181 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1113 through 1121 removed outlier: 7.115A pdb=" N VAL B1131 " --> pdb=" O ILE B1115 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER B1117 " --> pdb=" O PHE B1129 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B1129 " --> pdb=" O SER B1117 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B1119 " --> pdb=" O TYR B1127 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B1127 " --> pdb=" O VAL B1119 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN B1121 " --> pdb=" O GLY B1125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY B1125 " --> pdb=" O ASN B1121 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN B 777 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS B1138 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B1140 " --> pdb=" O GLN B 773 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 773 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR B1142 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 771 " --> pdb=" O THR B1142 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 771 " --> pdb=" O ALA C 961 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AE4, first strand: chain 'B' and resid 1196 through 1199 removed outlier: 4.155A pdb=" N CYS B1156 " --> pdb=" O VAL B1199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE6, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.314A pdb=" N ARG C 343 " --> pdb=" O ASP C 334 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 83 through 85 removed outlier: 7.045A pdb=" N ALA C 320 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY C 128 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 322 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 270 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER C 275 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU C 288 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.552A pdb=" N ARG C 146 " --> pdb=" O TYR C 135 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AF1, first strand: chain 'C' and resid 240 through 243 removed outlier: 4.339A pdb=" N LEU C 195 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN C 174 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N TYR C 172 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 173 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE C 161 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N HIS C 175 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA C 159 " --> pdb=" O HIS C 175 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 214 through 216 removed outlier: 6.393A pdb=" N ILE C 214 " --> pdb=" O SER C 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 367 through 371 removed outlier: 4.195A pdb=" N LEU C 658 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.986A pdb=" N SER C 448 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 575 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 485 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N CYS C 433 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 487 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C 431 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 489 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 416 through 417 Processing sheet with id=AF6, first strand: chain 'C' and resid 519 through 520 removed outlier: 3.541A pdb=" N TRP C 506 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C 556 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS C 510 " --> pdb=" O VAL C 554 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 554 " --> pdb=" O CYS C 510 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 553 " --> pdb=" O ASP C 548 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 716 through 722 removed outlier: 6.781A pdb=" N VAL C 716 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL C 753 " --> pdb=" O VAL C 716 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N SER C 718 " --> pdb=" O VAL C 753 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 794 through 796 Processing sheet with id=AF9, first strand: chain 'C' and resid 1196 through 1199 removed outlier: 4.245A pdb=" N CYS C1156 " --> pdb=" O VAL C1199 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2796 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: 6.24 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4446 1.30 - 1.43: 7897 1.43 - 1.57: 15533 1.57 - 1.70: 2 1.70 - 1.83: 180 Bond restraints: 28058 Sorted by residual: bond pdb=" CA CYS C 245 " pdb=" C CYS C 245 " ideal model delta sigma weight residual 1.524 1.430 0.094 1.35e-02 5.49e+03 4.90e+01 bond pdb=" CA LEU B 84 " pdb=" C LEU B 84 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.20e-02 6.94e+03 4.58e+01 bond pdb=" CA LYS B 512 " pdb=" C LYS B 512 " ideal model delta sigma weight residual 1.522 1.442 0.079 1.22e-02 6.72e+03 4.23e+01 bond pdb=" CA GLN B 465 " pdb=" C GLN B 465 " ideal model delta sigma weight residual 1.525 1.444 0.081 1.28e-02 6.10e+03 3.97e+01 bond pdb=" CA ASP A 894 " pdb=" C ASP A 894 " ideal model delta sigma weight residual 1.523 1.451 0.071 1.17e-02 7.31e+03 3.73e+01 ... (remaining 28053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 37011 2.67 - 5.33: 954 5.33 - 8.00: 139 8.00 - 10.67: 35 10.67 - 13.33: 9 Bond angle restraints: 38148 Sorted by residual: angle pdb=" N SER C 642 " pdb=" CA SER C 642 " pdb=" C SER C 642 " ideal model delta sigma weight residual 110.53 123.86 -13.33 1.32e+00 5.74e-01 1.02e+02 angle pdb=" N GLY C 348 " pdb=" CA GLY C 348 " pdb=" C GLY C 348 " ideal model delta sigma weight residual 112.73 124.31 -11.58 1.20e+00 6.94e-01 9.31e+01 angle pdb=" N TYR B 209 " pdb=" CA TYR B 209 " pdb=" C TYR B 209 " ideal model delta sigma weight residual 110.23 122.51 -12.28 1.45e+00 4.76e-01 7.17e+01 angle pdb=" N PHE B 920 " pdb=" CA PHE B 920 " pdb=" C PHE B 920 " ideal model delta sigma weight residual 111.28 120.50 -9.22 1.09e+00 8.42e-01 7.15e+01 angle pdb=" N GLN A 466 " pdb=" CA GLN A 466 " pdb=" C GLN A 466 " ideal model delta sigma weight residual 111.37 123.85 -12.48 1.65e+00 3.67e-01 5.72e+01 ... (remaining 38143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 16046 21.90 - 43.81: 1328 43.81 - 65.71: 254 65.71 - 87.62: 83 87.62 - 109.52: 26 Dihedral angle restraints: 17737 sinusoidal: 7879 harmonic: 9858 Sorted by residual: dihedral pdb=" CB CYS B 619 " pdb=" SG CYS B 619 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 4.28 88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 602 " pdb=" SG CYS C 602 " pdb=" SG CYS C 653 " pdb=" CB CYS C 653 " ideal model delta sinusoidal sigma weight residual -86.00 1.04 -87.04 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 619 " pdb=" SG CYS A 619 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -12.00 -74.00 1 1.00e+01 1.00e-02 6.95e+01 ... (remaining 17734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4044 0.098 - 0.197: 363 0.197 - 0.295: 41 0.295 - 0.394: 8 0.394 - 0.492: 1 Chirality restraints: 4457 Sorted by residual: chirality pdb=" CA PHE C 289 " pdb=" N PHE C 289 " pdb=" C PHE C 289 " pdb=" CB PHE C 289 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA SER A 447 " pdb=" N SER A 447 " pdb=" C SER A 447 " pdb=" CB SER A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA SER C 642 " pdb=" N SER C 642 " pdb=" C SER C 642 " pdb=" CB SER C 642 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4454 not shown) Planarity restraints: 4911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 204 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C PRO B 204 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO B 204 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU B 205 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 73 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLY C 73 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY C 73 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU C 74 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C1122 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.09e+01 pdb=" N PRO C1123 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C1123 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C1123 " 0.045 5.00e-02 4.00e+02 ... (remaining 4908 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2279 2.74 - 3.28: 24644 3.28 - 3.82: 45192 3.82 - 4.36: 54636 4.36 - 4.90: 96247 Nonbonded interactions: 222998 Sorted by model distance: nonbonded pdb=" OH TYR B 417 " pdb=" OH TYR B 446 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR C 417 " pdb=" OH TYR C 446 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 169 " pdb=" OH TYR A 209 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 417 " pdb=" OH TYR A 446 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG B 168 " pdb=" O ASN B 207 " model vdw 2.276 3.120 ... (remaining 222993 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 18 through 1218 or resid 1402 through 1412)) selection = (chain 'B' and (resid 18 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 1218 or resid 1402 through 1412 \ )) selection = (chain 'C' and (resid 18 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 1218 or resid 1402 through 1412 \ )) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.700 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.009 0.094 28188 Z= 0.608 Angle : 0.984 13.332 38484 Z= 0.591 Chirality : 0.059 0.492 4457 Planarity : 0.006 0.082 4857 Dihedral : 16.935 109.520 11263 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.78 % Allowed : 19.27 % Favored : 78.95 % Cbeta Deviations : 0.16 % 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 aren not related in a simple way. whole: -0.76 (0.13), residues: 3297 helix: -0.21 (0.18), residues: 705 sheet: 0.33 (0.18), residues: 789 loop : -0.99 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 628 TYR 0.031 0.002 TYR B 924 PHE 0.051 0.002 PHE A 454 TRP 0.007 0.001 TRP C 318 HIS 0.006 0.001 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.00878 (28058) covalent geometry : angle 0.97294 (38148) SS BOND : bond 0.00877 ( 54) SS BOND : angle 1.83915 ( 108) hydrogen bonds : bond 0.22250 ( 1001) hydrogen bonds : angle 8.32067 ( 2796) link_BETA1-4 : bond 0.00510 ( 22) link_BETA1-4 : angle 1.74533 ( 66) link_NAG-ASN : bond 0.00316 ( 54) link_NAG-ASN : angle 1.91616 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.899 Fit side-chains REVERT: A 196 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8459 (pt) REVERT: A 446 TYR cc_start: 0.9501 (OUTLIER) cc_final: 0.8123 (p90) REVERT: A 496 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6986 (tp) REVERT: A 543 TYR cc_start: 0.8490 (m-80) cc_final: 0.8259 (m-80) REVERT: A 905 MET cc_start: 0.6829 (mmt) cc_final: 0.6591 (mmm) REVERT: A 906 GLN cc_start: 0.6249 (mt0) cc_final: 0.6027 (pp30) REVERT: A 935 MET cc_start: 0.8702 (ttt) cc_final: 0.8441 (tpp) REVERT: A 944 LEU cc_start: 0.8457 (tm) cc_final: 0.8225 (tp) REVERT: A 988 GLN cc_start: 0.7611 (mp-120) cc_final: 0.7373 (mt0) REVERT: A 1054 GLU cc_start: 0.7750 (tt0) cc_final: 0.7423 (mp0) REVERT: A 1082 GLU cc_start: 0.7962 (mp0) cc_final: 0.7613 (tt0) REVERT: B 446 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.7878 (p90) REVERT: B 466 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8480 (pt0) REVERT: B 505 ASN cc_start: 0.8695 (m110) cc_final: 0.8472 (m110) REVERT: B 548 ASP cc_start: 0.8208 (t0) cc_final: 0.7701 (t0) REVERT: B 550 ILE cc_start: 0.8945 (mm) cc_final: 0.8645 (mm) REVERT: B 848 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7988 (mm110) REVERT: B 898 MET cc_start: 0.8946 (ttp) cc_final: 0.8613 (ttp) REVERT: B 972 MET cc_start: 0.9039 (mtp) cc_final: 0.8753 (mtm) REVERT: B 995 GLN cc_start: 0.8105 (mt0) cc_final: 0.7780 (mt0) REVERT: B 1000 MET cc_start: 0.8875 (ptt) cc_final: 0.8565 (ptt) REVERT: B 1016 ASP cc_start: 0.8054 (m-30) cc_final: 0.7807 (m-30) REVERT: B 1056 GLU cc_start: 0.8152 (mp0) cc_final: 0.7779 (mp0) REVERT: C 253 ILE cc_start: 0.8485 (pt) cc_final: 0.8280 (pt) REVERT: C 972 MET cc_start: 0.9154 (mtp) cc_final: 0.8838 (ttm) REVERT: C 995 GLN cc_start: 0.8300 (mt0) cc_final: 0.7799 (mt0) REVERT: C 1160 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7445 (pp) outliers start: 52 outliers final: 10 residues processed: 264 average time/residue: 0.5252 time to fit residues: 165.9555 Evaluate side-chains 173 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 1160 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 465 GLN A 495 ASN A 773 GLN A 875 GLN A 966 GLN A 998 ASN B 285 ASN B 416 ASN B 760 HIS B 899 GLN C 219 HIS C 495 ASN C 505 ASN C 766 ASN C 773 GLN C 851 GLN C1077 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098920 restraints weight = 36008.398| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.04 r_work: 0.2983 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28188 Z= 0.126 Angle : 0.558 8.974 38484 Z= 0.291 Chirality : 0.044 0.168 4457 Planarity : 0.005 0.073 4857 Dihedral : 9.369 70.394 5317 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.84 % Allowed : 18.66 % Favored : 78.50 % 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 aren not related in a simple way. whole: 0.09 (0.14), residues: 3297 helix: 1.47 (0.20), residues: 687 sheet: 0.68 (0.19), residues: 729 loop : -0.74 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 651 TYR 0.020 0.001 TYR B 135 PHE 0.015 0.001 PHE A 247 TRP 0.005 0.001 TRP B 215 HIS 0.009 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00277 (28058) covalent geometry : angle 0.54120 (38148) SS BOND : bond 0.00335 ( 54) SS BOND : angle 1.12513 ( 108) hydrogen bonds : bond 0.05062 ( 1001) hydrogen bonds : angle 5.49874 ( 2796) link_BETA1-4 : bond 0.00337 ( 22) link_BETA1-4 : angle 2.03151 ( 66) link_NAG-ASN : bond 0.00227 ( 54) link_NAG-ASN : angle 1.58824 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 181 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 446 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8806 (p90) REVERT: A 543 TYR cc_start: 0.8573 (m-80) cc_final: 0.8371 (m-80) REVERT: A 651 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7706 (mtt180) REVERT: A 905 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6677 (mmm) REVERT: A 906 GLN cc_start: 0.6501 (mt0) cc_final: 0.6262 (pp30) REVERT: A 935 MET cc_start: 0.8778 (ttt) cc_final: 0.8519 (tpp) REVERT: A 944 LEU cc_start: 0.8526 (tm) cc_final: 0.8292 (tp) REVERT: A 988 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: A 1054 GLU cc_start: 0.7848 (tt0) cc_final: 0.7544 (mp0) REVERT: B 233 LEU cc_start: 0.9166 (tp) cc_final: 0.8897 (tp) REVERT: B 446 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8470 (p90) REVERT: B 505 ASN cc_start: 0.8521 (m110) cc_final: 0.8237 (m110) REVERT: B 848 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8221 (mm110) REVERT: B 972 MET cc_start: 0.9174 (mtp) cc_final: 0.8943 (mtm) REVERT: B 980 GLN cc_start: 0.8300 (tt0) cc_final: 0.7966 (tt0) REVERT: B 995 GLN cc_start: 0.8346 (mt0) cc_final: 0.8137 (mt0) REVERT: B 1000 MET cc_start: 0.9014 (ptt) cc_final: 0.8587 (ptt) REVERT: B 1056 GLU cc_start: 0.8400 (mp0) cc_final: 0.8161 (mp0) REVERT: C 138 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6580 (mp) REVERT: C 396 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8910 (ttp) REVERT: C 446 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8377 (p90) REVERT: C 626 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: C 760 HIS cc_start: 0.7668 (t-90) cc_final: 0.7314 (t-170) REVERT: C 812 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8839 (mt) REVERT: C 972 MET cc_start: 0.9350 (mtp) cc_final: 0.9108 (ttm) REVERT: C 995 GLN cc_start: 0.8560 (mt0) cc_final: 0.8051 (mt0) REVERT: C 1197 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7926 (ptt-90) outliers start: 83 outliers final: 23 residues processed: 243 average time/residue: 0.5084 time to fit residues: 148.5871 Evaluate side-chains 186 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 1007 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 626 GLN Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 248 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 416 ASN B 760 HIS B 995 GLN C 175 HIS C 495 ASN C 851 GLN C 966 GLN C1138 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094483 restraints weight = 36137.095| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.93 r_work: 0.2915 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28188 Z= 0.215 Angle : 0.620 15.361 38484 Z= 0.316 Chirality : 0.046 0.170 4457 Planarity : 0.005 0.076 4857 Dihedral : 7.967 59.249 5299 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.77 % Allowed : 18.90 % Favored : 78.33 % 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 aren not related in a simple way. whole: 0.15 (0.14), residues: 3297 helix: 1.80 (0.20), residues: 687 sheet: 0.40 (0.18), residues: 762 loop : -0.69 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1197 TYR 0.017 0.002 TYR C 816 PHE 0.017 0.002 PHE A 454 TRP 0.006 0.001 TRP B1178 HIS 0.008 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00517 (28058) covalent geometry : angle 0.60170 (38148) SS BOND : bond 0.00500 ( 54) SS BOND : angle 1.26252 ( 108) hydrogen bonds : bond 0.05429 ( 1001) hydrogen bonds : angle 5.31854 ( 2796) link_BETA1-4 : bond 0.00358 ( 22) link_BETA1-4 : angle 2.18070 ( 66) link_NAG-ASN : bond 0.00223 ( 54) link_NAG-ASN : angle 1.77166 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 159 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 466 GLN cc_start: 0.8618 (mt0) cc_final: 0.8377 (mt0) REVERT: A 543 TYR cc_start: 0.8710 (m-80) cc_final: 0.8503 (m-80) REVERT: A 906 GLN cc_start: 0.6506 (mt0) cc_final: 0.6202 (pp30) REVERT: A 944 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 1056 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7954 (mp0) REVERT: A 1160 ILE cc_start: 0.9048 (mt) cc_final: 0.8831 (mp) REVERT: B 233 LEU cc_start: 0.9175 (tp) cc_final: 0.8889 (tp) REVERT: B 446 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.8584 (p90) REVERT: B 586 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8766 (mtt) REVERT: B 731 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 848 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8432 (mm-40) REVERT: B 972 MET cc_start: 0.9214 (mtp) cc_final: 0.8972 (mtm) REVERT: B 980 GLN cc_start: 0.8348 (tt0) cc_final: 0.8083 (tt0) REVERT: B 1000 MET cc_start: 0.8991 (ptt) cc_final: 0.8582 (ptt) REVERT: B 1056 GLU cc_start: 0.8162 (mp0) cc_final: 0.7917 (mp0) REVERT: C 396 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8908 (ttp) REVERT: C 432 SER cc_start: 0.9352 (OUTLIER) cc_final: 0.9077 (t) REVERT: C 446 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8345 (p90) REVERT: C 760 HIS cc_start: 0.7606 (t-90) cc_final: 0.7207 (t-170) REVERT: C 812 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8866 (mt) REVERT: C 995 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: C 1197 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7966 (ptt-90) outliers start: 81 outliers final: 40 residues processed: 219 average time/residue: 0.5088 time to fit residues: 134.4478 Evaluate side-chains 191 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 1007 THR Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 626 GLN Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1023 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 234 optimal weight: 9.9990 chunk 268 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 322 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 495 ASN A 966 GLN B 416 ASN B 760 HIS C 220 GLN C 495 ASN C 505 ASN C 851 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096908 restraints weight = 36098.525| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.93 r_work: 0.3017 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28188 Z= 0.103 Angle : 0.524 10.339 38484 Z= 0.270 Chirality : 0.043 0.194 4457 Planarity : 0.004 0.067 4857 Dihedral : 6.577 58.979 5299 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.60 % Allowed : 19.00 % Favored : 78.40 % 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 aren not related in a simple way. whole: 0.38 (0.14), residues: 3297 helix: 2.17 (0.20), residues: 687 sheet: 0.58 (0.19), residues: 738 loop : -0.62 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 651 TYR 0.022 0.001 TYR B 282 PHE 0.012 0.001 PHE B 123 TRP 0.006 0.001 TRP B 506 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00227 (28058) covalent geometry : angle 0.50600 (38148) SS BOND : bond 0.00317 ( 54) SS BOND : angle 1.14247 ( 108) hydrogen bonds : bond 0.04116 ( 1001) hydrogen bonds : angle 4.98989 ( 2796) link_BETA1-4 : bond 0.00356 ( 22) link_BETA1-4 : angle 1.97374 ( 66) link_NAG-ASN : bond 0.00208 ( 54) link_NAG-ASN : angle 1.56350 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 159 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 GLN cc_start: 0.8494 (mt0) cc_final: 0.8245 (mt0) REVERT: A 841 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8721 (tt) REVERT: A 944 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (tp) REVERT: B 233 LEU cc_start: 0.9120 (tp) cc_final: 0.8792 (tp) REVERT: B 280 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8286 (t0) REVERT: B 446 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.8562 (p90) REVERT: B 586 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8972 (mmm) REVERT: B 848 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8279 (mm110) REVERT: B 972 MET cc_start: 0.9134 (mtp) cc_final: 0.8869 (mtm) REVERT: B 984 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: B 1000 MET cc_start: 0.8895 (ptt) cc_final: 0.8450 (ptt) REVERT: B 1056 GLU cc_start: 0.8185 (mp0) cc_final: 0.7902 (mp0) REVERT: B 1082 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: C 146 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.5130 (mpt180) REVERT: C 396 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8829 (ttp) REVERT: C 432 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8979 (t) REVERT: C 446 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8465 (p90) REVERT: C 760 HIS cc_start: 0.7564 (t-90) cc_final: 0.7191 (t-170) REVERT: C 812 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8864 (mt) REVERT: C 995 GLN cc_start: 0.8608 (mt0) cc_final: 0.8089 (mt0) REVERT: C 1124 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7456 (t0) outliers start: 76 outliers final: 30 residues processed: 217 average time/residue: 0.5227 time to fit residues: 136.0980 Evaluate side-chains 181 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 81 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 14 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 966 GLN A 979 GLN A 988 GLN B 41 GLN B 760 HIS C 495 ASN C 505 ASN C 851 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099355 restraints weight = 35742.354| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.86 r_work: 0.3017 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28188 Z= 0.119 Angle : 0.524 8.651 38484 Z= 0.269 Chirality : 0.043 0.248 4457 Planarity : 0.004 0.066 4857 Dihedral : 6.107 58.250 5299 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.98 % Allowed : 18.49 % Favored : 78.53 % 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 aren not related in a simple way. whole: 0.41 (0.14), residues: 3297 helix: 2.28 (0.20), residues: 687 sheet: 0.44 (0.18), residues: 786 loop : -0.60 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 651 TYR 0.015 0.001 TYR B 282 PHE 0.012 0.001 PHE B 123 TRP 0.006 0.001 TRP C 44 HIS 0.007 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00275 (28058) covalent geometry : angle 0.50600 (38148) SS BOND : bond 0.00416 ( 54) SS BOND : angle 1.15652 ( 108) hydrogen bonds : bond 0.04122 ( 1001) hydrogen bonds : angle 4.87450 ( 2796) link_BETA1-4 : bond 0.00380 ( 22) link_BETA1-4 : angle 2.02595 ( 66) link_NAG-ASN : bond 0.00185 ( 54) link_NAG-ASN : angle 1.55097 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 155 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9178 (m) cc_final: 0.8796 (p) REVERT: A 466 GLN cc_start: 0.8484 (mt0) cc_final: 0.8235 (mt0) REVERT: A 841 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 944 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 966 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (mp-120) REVERT: A 1056 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7655 (mp0) REVERT: B 233 LEU cc_start: 0.9142 (tp) cc_final: 0.8796 (tp) REVERT: B 446 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.8590 (p90) REVERT: B 586 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8908 (mmm) REVERT: B 731 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8916 (tt) REVERT: B 848 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8329 (mm110) REVERT: B 972 MET cc_start: 0.9115 (mtp) cc_final: 0.8855 (mtm) REVERT: B 984 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 1000 MET cc_start: 0.8879 (ptt) cc_final: 0.8411 (ptt) REVERT: B 1056 GLU cc_start: 0.8167 (mp0) cc_final: 0.7908 (mp0) REVERT: C 84 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8862 (tp) REVERT: C 396 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8876 (ttp) REVERT: C 432 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.8945 (t) REVERT: C 446 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8379 (p90) REVERT: C 760 HIS cc_start: 0.7563 (t-90) cc_final: 0.7146 (t-170) REVERT: C 812 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9074 (mt) REVERT: C 995 GLN cc_start: 0.8651 (mt0) cc_final: 0.8136 (mt0) REVERT: C 1124 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7518 (t0) outliers start: 87 outliers final: 43 residues processed: 220 average time/residue: 0.5046 time to fit residues: 133.7391 Evaluate side-chains 197 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 966 GLN Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1193 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 294 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN B 416 ASN B 760 HIS C 495 ASN C 851 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096121 restraints weight = 36119.985| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.88 r_work: 0.2937 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28188 Z= 0.168 Angle : 0.561 9.209 38484 Z= 0.287 Chirality : 0.044 0.225 4457 Planarity : 0.004 0.070 4857 Dihedral : 6.070 58.680 5299 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.12 % Allowed : 18.42 % Favored : 78.47 % 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 aren not related in a simple way. whole: 0.38 (0.14), residues: 3297 helix: 2.25 (0.20), residues: 687 sheet: 0.42 (0.19), residues: 753 loop : -0.58 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 651 TYR 0.016 0.001 TYR B 282 PHE 0.013 0.001 PHE B 123 TRP 0.006 0.001 TRP C 318 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00402 (28058) covalent geometry : angle 0.54042 (38148) SS BOND : bond 0.00463 ( 54) SS BOND : angle 1.49506 ( 108) hydrogen bonds : bond 0.04537 ( 1001) hydrogen bonds : angle 4.91335 ( 2796) link_BETA1-4 : bond 0.00330 ( 22) link_BETA1-4 : angle 2.09828 ( 66) link_NAG-ASN : bond 0.00195 ( 54) link_NAG-ASN : angle 1.64201 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 143 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9249 (m) cc_final: 0.8841 (p) REVERT: A 466 GLN cc_start: 0.8536 (mt0) cc_final: 0.8273 (mt0) REVERT: A 841 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8722 (tt) REVERT: A 944 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8200 (tp) REVERT: A 988 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 1056 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7791 (mp0) REVERT: B 233 LEU cc_start: 0.9054 (tp) cc_final: 0.8741 (tp) REVERT: B 422 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 446 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.8540 (p90) REVERT: B 586 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8945 (mmm) REVERT: B 731 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 848 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8386 (mm-40) REVERT: B 972 MET cc_start: 0.9189 (mtp) cc_final: 0.8927 (mtm) REVERT: B 984 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 1000 MET cc_start: 0.8880 (ptt) cc_final: 0.8452 (ptt) REVERT: B 1056 GLU cc_start: 0.8177 (mp0) cc_final: 0.7879 (mp0) REVERT: C 84 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8886 (tp) REVERT: C 396 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8979 (ttp) REVERT: C 432 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9022 (t) REVERT: C 446 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8329 (p90) REVERT: C 512 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8142 (tttm) REVERT: C 760 HIS cc_start: 0.7550 (t-90) cc_final: 0.7023 (t-170) REVERT: C 812 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9007 (mt) REVERT: C 995 GLN cc_start: 0.8603 (mt0) cc_final: 0.8105 (mt0) REVERT: C 1052 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7880 (Cg_endo) REVERT: C 1124 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7588 (t0) outliers start: 91 outliers final: 50 residues processed: 214 average time/residue: 0.4585 time to fit residues: 118.5093 Evaluate side-chains 200 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 135 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1193 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 626 GLN Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 126 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 249 optimal weight: 0.3980 chunk 284 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 272 optimal weight: 0.0980 chunk 304 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 988 GLN B 41 GLN B 495 ASN B 760 HIS C 495 ASN C 505 ASN C 851 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097915 restraints weight = 35750.153| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.06 r_work: 0.2984 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28188 Z= 0.109 Angle : 0.515 8.272 38484 Z= 0.265 Chirality : 0.043 0.194 4457 Planarity : 0.004 0.067 4857 Dihedral : 5.715 58.260 5299 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.77 % Allowed : 18.73 % Favored : 78.50 % 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 aren not related in a simple way. whole: 0.44 (0.14), residues: 3297 helix: 2.37 (0.20), residues: 687 sheet: 0.40 (0.18), residues: 786 loop : -0.57 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 651 TYR 0.014 0.001 TYR B 282 PHE 0.012 0.001 PHE B 123 TRP 0.005 0.001 TRP C 318 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00251 (28058) covalent geometry : angle 0.49698 (38148) SS BOND : bond 0.00343 ( 54) SS BOND : angle 1.22123 ( 108) hydrogen bonds : bond 0.04015 ( 1001) hydrogen bonds : angle 4.78023 ( 2796) link_BETA1-4 : bond 0.00360 ( 22) link_BETA1-4 : angle 1.93656 ( 66) link_NAG-ASN : bond 0.00187 ( 54) link_NAG-ASN : angle 1.55067 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 146 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9199 (m) cc_final: 0.8828 (p) REVERT: A 466 GLN cc_start: 0.8491 (mt0) cc_final: 0.8234 (mt0) REVERT: A 841 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 1056 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7750 (mp0) REVERT: B 233 LEU cc_start: 0.9127 (tp) cc_final: 0.8786 (tp) REVERT: B 422 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 446 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.8578 (p90) REVERT: B 586 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (mmm) REVERT: B 731 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8899 (tt) REVERT: B 848 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8321 (mm110) REVERT: B 972 MET cc_start: 0.9117 (mtp) cc_final: 0.8851 (mtm) REVERT: B 984 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 1000 MET cc_start: 0.8853 (ptt) cc_final: 0.8388 (ptt) REVERT: B 1056 GLU cc_start: 0.8181 (mp0) cc_final: 0.7902 (mp0) REVERT: B 1082 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: C 84 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8880 (tp) REVERT: C 396 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8996 (ttp) REVERT: C 432 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8956 (t) REVERT: C 446 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8424 (p90) REVERT: C 760 HIS cc_start: 0.7652 (t-90) cc_final: 0.7145 (t70) REVERT: C 812 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9053 (mt) REVERT: C 986 GLN cc_start: 0.7723 (tp40) cc_final: 0.7302 (tt0) REVERT: C 995 GLN cc_start: 0.8650 (mt0) cc_final: 0.8122 (mt0) REVERT: C 1076 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8331 (tm-30) outliers start: 81 outliers final: 49 residues processed: 209 average time/residue: 0.4752 time to fit residues: 120.4721 Evaluate side-chains 199 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1193 MET Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Chi-restraints excluded: chain C residue 1076 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 277 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 264 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN B 495 ASN B 760 HIS C 495 ASN C 851 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097391 restraints weight = 36047.306| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.04 r_work: 0.3017 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28188 Z= 0.132 Angle : 0.532 9.498 38484 Z= 0.273 Chirality : 0.043 0.188 4457 Planarity : 0.004 0.067 4857 Dihedral : 5.630 57.810 5299 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.70 % Allowed : 18.97 % Favored : 78.33 % 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 aren not related in a simple way. whole: 0.45 (0.14), residues: 3297 helix: 2.43 (0.20), residues: 684 sheet: 0.47 (0.19), residues: 756 loop : -0.59 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 651 TYR 0.013 0.001 TYR B 282 PHE 0.012 0.001 PHE B 123 TRP 0.005 0.001 TRP B 506 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00313 (28058) covalent geometry : angle 0.51294 (38148) SS BOND : bond 0.00391 ( 54) SS BOND : angle 1.32508 ( 108) hydrogen bonds : bond 0.04158 ( 1001) hydrogen bonds : angle 4.77612 ( 2796) link_BETA1-4 : bond 0.00350 ( 22) link_BETA1-4 : angle 1.95513 ( 66) link_NAG-ASN : bond 0.00184 ( 54) link_NAG-ASN : angle 1.57603 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 142 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9198 (m) cc_final: 0.8827 (p) REVERT: A 466 GLN cc_start: 0.8491 (mt0) cc_final: 0.8258 (mt0) REVERT: A 841 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 233 LEU cc_start: 0.9164 (tp) cc_final: 0.8830 (tp) REVERT: B 422 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 446 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.8582 (p90) REVERT: B 586 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8915 (mmm) REVERT: B 848 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8401 (mm-40) REVERT: B 972 MET cc_start: 0.9201 (mtp) cc_final: 0.8943 (mtm) REVERT: B 984 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 1000 MET cc_start: 0.8856 (ptt) cc_final: 0.8412 (ptt) REVERT: B 1056 GLU cc_start: 0.8196 (mp0) cc_final: 0.7923 (mp0) REVERT: B 1082 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: C 84 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8902 (tp) REVERT: C 396 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.9004 (ttp) REVERT: C 432 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8943 (t) REVERT: C 446 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8369 (p90) REVERT: C 760 HIS cc_start: 0.7731 (t-90) cc_final: 0.7284 (t70) REVERT: C 812 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9101 (mt) REVERT: C 995 GLN cc_start: 0.8675 (mt0) cc_final: 0.8205 (mt0) outliers start: 79 outliers final: 51 residues processed: 206 average time/residue: 0.4288 time to fit residues: 108.0643 Evaluate side-chains 198 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1193 MET Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 156 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 165 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 851 GLN B 495 ASN B 760 HIS C 495 ASN C 851 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097468 restraints weight = 35964.234| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.01 r_work: 0.3021 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28188 Z= 0.116 Angle : 0.533 11.366 38484 Z= 0.274 Chirality : 0.043 0.186 4457 Planarity : 0.004 0.066 4857 Dihedral : 5.542 57.512 5299 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.60 % Allowed : 18.90 % Favored : 78.50 % 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 aren not related in a simple way. whole: 0.48 (0.14), residues: 3297 helix: 2.49 (0.20), residues: 684 sheet: 0.47 (0.19), residues: 756 loop : -0.59 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 651 TYR 0.012 0.001 TYR B 282 PHE 0.015 0.001 PHE B 247 TRP 0.005 0.001 TRP B 506 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00269 (28058) covalent geometry : angle 0.51240 (38148) SS BOND : bond 0.00373 ( 54) SS BOND : angle 1.65147 ( 108) hydrogen bonds : bond 0.03970 ( 1001) hydrogen bonds : angle 4.72800 ( 2796) link_BETA1-4 : bond 0.00369 ( 22) link_BETA1-4 : angle 1.87563 ( 66) link_NAG-ASN : bond 0.00184 ( 54) link_NAG-ASN : angle 1.53343 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 141 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9192 (m) cc_final: 0.8812 (p) REVERT: A 466 GLN cc_start: 0.8481 (mt0) cc_final: 0.8229 (mt0) REVERT: A 841 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 1056 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7440 (mp0) REVERT: B 233 LEU cc_start: 0.9171 (tp) cc_final: 0.8822 (tp) REVERT: B 422 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 446 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.8587 (p90) REVERT: B 586 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8904 (mmm) REVERT: B 848 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8393 (mm-40) REVERT: B 972 MET cc_start: 0.9134 (mtp) cc_final: 0.8932 (mtm) REVERT: B 984 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: B 1000 MET cc_start: 0.8846 (ptt) cc_final: 0.8399 (ptt) REVERT: B 1056 GLU cc_start: 0.8200 (mp0) cc_final: 0.7928 (mp0) REVERT: C 84 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8895 (tp) REVERT: C 146 ARG cc_start: 0.5716 (OUTLIER) cc_final: 0.4687 (mpt-90) REVERT: C 396 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.9010 (ttp) REVERT: C 432 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.8923 (t) REVERT: C 446 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8395 (p90) REVERT: C 760 HIS cc_start: 0.7733 (t-90) cc_final: 0.7321 (t70) REVERT: C 812 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9116 (mt) REVERT: C 986 GLN cc_start: 0.7788 (tp40) cc_final: 0.7391 (tt0) REVERT: C 995 GLN cc_start: 0.8669 (mt0) cc_final: 0.8144 (mt0) outliers start: 76 outliers final: 51 residues processed: 201 average time/residue: 0.4718 time to fit residues: 115.0043 Evaluate side-chains 198 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1193 MET Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 53 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN B 495 ASN B 760 HIS C 773 GLN C 851 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095866 restraints weight = 35976.085| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.99 r_work: 0.2996 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28188 Z= 0.158 Angle : 0.564 11.328 38484 Z= 0.288 Chirality : 0.044 0.187 4457 Planarity : 0.004 0.066 4857 Dihedral : 5.678 57.599 5299 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.26 % Allowed : 19.34 % Favored : 78.40 % 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 aren not related in a simple way. whole: 0.39 (0.14), residues: 3297 helix: 2.36 (0.20), residues: 693 sheet: 0.40 (0.19), residues: 756 loop : -0.63 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 651 TYR 0.012 0.001 TYR C 135 PHE 0.014 0.001 PHE B 191 TRP 0.006 0.001 TRP B 506 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00381 (28058) covalent geometry : angle 0.54361 (38148) SS BOND : bond 0.00492 ( 54) SS BOND : angle 1.63711 ( 108) hydrogen bonds : bond 0.04416 ( 1001) hydrogen bonds : angle 4.81560 ( 2796) link_BETA1-4 : bond 0.00326 ( 22) link_BETA1-4 : angle 1.97999 ( 66) link_NAG-ASN : bond 0.00189 ( 54) link_NAG-ASN : angle 1.63383 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 135 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9208 (m) cc_final: 0.8819 (p) REVERT: A 466 GLN cc_start: 0.8512 (mt0) cc_final: 0.8268 (mt0) REVERT: A 841 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8790 (tt) REVERT: A 1056 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7549 (mp0) REVERT: B 233 LEU cc_start: 0.9186 (tp) cc_final: 0.8869 (tp) REVERT: B 422 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (mt) REVERT: B 446 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.8507 (p90) REVERT: B 586 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: B 731 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 848 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8337 (mm110) REVERT: B 972 MET cc_start: 0.9223 (mtp) cc_final: 0.8957 (mtm) REVERT: B 984 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: B 1000 MET cc_start: 0.8892 (ptt) cc_final: 0.8486 (ptt) REVERT: B 1056 GLU cc_start: 0.8212 (mp0) cc_final: 0.7899 (mp0) REVERT: C 84 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8918 (tp) REVERT: C 396 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9019 (ttp) REVERT: C 432 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8962 (t) REVERT: C 446 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8445 (p90) REVERT: C 512 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8152 (tttm) REVERT: C 760 HIS cc_start: 0.7768 (t-90) cc_final: 0.7325 (t70) REVERT: C 812 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9104 (mt) REVERT: C 986 GLN cc_start: 0.7845 (tp40) cc_final: 0.7440 (tt0) outliers start: 66 outliers final: 47 residues processed: 189 average time/residue: 0.4380 time to fit residues: 100.9940 Evaluate side-chains 194 residues out of total 2922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 940 THR Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1023 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 188 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 248 optimal weight: 0.0170 chunk 97 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 191 optimal weight: 0.2980 chunk 93 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN B 495 ASN B 505 ASN B 760 HIS C 851 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098976 restraints weight = 35736.682| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.99 r_work: 0.3027 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28188 Z= 0.096 Angle : 0.509 9.730 38484 Z= 0.262 Chirality : 0.042 0.180 4457 Planarity : 0.004 0.065 4857 Dihedral : 5.310 56.936 5299 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.05 % Allowed : 19.48 % Favored : 78.47 % 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 aren not related in a simple way. whole: 0.49 (0.15), residues: 3297 helix: 2.52 (0.20), residues: 693 sheet: 0.37 (0.18), residues: 786 loop : -0.56 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 651 TYR 0.011 0.001 TYR C 135 PHE 0.013 0.001 PHE B 191 TRP 0.005 0.001 TRP C 318 HIS 0.006 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00217 (28058) covalent geometry : angle 0.49135 (38148) SS BOND : bond 0.00350 ( 54) SS BOND : angle 1.44995 ( 108) hydrogen bonds : bond 0.03643 ( 1001) hydrogen bonds : angle 4.63631 ( 2796) link_BETA1-4 : bond 0.00368 ( 22) link_BETA1-4 : angle 1.70870 ( 66) link_NAG-ASN : bond 0.00200 ( 54) link_NAG-ASN : angle 1.47273 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6748.71 seconds wall clock time: 116 minutes 0.13 seconds (6960.13 seconds total)