Starting phenix.real_space_refine on Thu Nov 20 00:17:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9i_8784/11_2025/5w9i_8784.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9i_8784/11_2025/5w9i_8784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w9i_8784/11_2025/5w9i_8784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9i_8784/11_2025/5w9i_8784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w9i_8784/11_2025/5w9i_8784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9i_8784/11_2025/5w9i_8784.map" } resolution = 3.6 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= 0.004 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 147 5.16 5 C 18252 2.51 5 N 4752 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28896 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "D" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "F" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "H" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "J" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "K" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.84, per 1000 atoms: 0.24 Number of scatterers: 28896 At special positions: 0 Unit cell: (155.04, 155.04, 183.6, 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 147 16.00 O 5745 8.00 N 4752 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.99 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.07 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.09 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.14 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.09 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.28 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.01 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=1.89 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=2.02 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.09 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.09 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.12 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.08 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=1.92 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=1.88 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.03 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.04 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=2.01 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.04 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.09 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.13 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.06 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.20 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.14 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG B1401 " - " ASN B 236 " " NAG B1402 " - " ASN B 155 " " NAG B1403 " - " ASN B 166 " " NAG B1404 " - " ASN B 719 " " NAG B1405 " - " ASN B 619 " " NAG B1406 " - " ASN B 104 " " NAG E1401 " - " ASN E 774 " " NAG F1401 " - " ASN F 236 " " NAG F1402 " - " ASN F 719 " " NAG F1403 " - " ASN F 166 " " NAG F1404 " - " ASN F 155 " " NAG F1405 " - " ASN F 619 " " NAG F1406 " - " ASN F 104 " " NAG I1401 " - " ASN I 774 " " NAG J1401 " - " ASN J 104 " " NAG J1402 " - " ASN J 155 " " NAG J1403 " - " ASN J 719 " " NAG J1410 " - " ASN J 236 " " NAG J1411 " - " ASN J 619 " " NAG J1412 " - " ASN J 166 " " NAG M 1 " - " ASN A 785 " " NAG N 1 " - " ASN A 870 " " NAG O 1 " - " ASN A1213 " " NAG P 1 " - " ASN A1176 " " NAG Q 1 " - " ASN B 66 " " NAG R 1 " - " ASN B 244 " " NAG S 1 " - " ASN B 125 " " NAG T 1 " - " ASN E 785 " " NAG U 1 " - " ASN E1176 " " NAG V 1 " - " ASN E 870 " " NAG W 1 " - " ASN E1213 " " NAG X 1 " - " ASN F 66 " " NAG Y 1 " - " ASN F 244 " " NAG Z 1 " - " ASN F 125 " " NAG a 1 " - " ASN I1213 " " NAG b 1 " - " ASN I 870 " " NAG c 1 " - " ASN I 785 " " NAG d 1 " - " ASN I1176 " " NAG e 1 " - " ASN J 244 " " NAG f 1 " - " ASN J 66 " " NAG g 1 " - " ASN J 125 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 69 sheets defined 23.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.516A pdb=" N VAL A 810 " --> pdb=" O CYS A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.908A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 removed outlier: 4.070A pdb=" N ASP A 910 " --> pdb=" O GLN A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.502A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 955 removed outlier: 3.663A pdb=" N ILE A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.867A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.236A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.923A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 675 through 678 removed outlier: 4.387A pdb=" N ALA B 678 " --> pdb=" O GLY B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 675 through 678' Processing helix chain 'B' and resid 694 through 702 removed outlier: 3.560A pdb=" N LYS B 698 " --> pdb=" O ARG B 694 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.617A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 805 through 810 removed outlier: 3.814A pdb=" N VAL E 810 " --> pdb=" O CYS E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 824 through 854 removed outlier: 3.898A pdb=" N CYS E 828 " --> pdb=" O TYR E 824 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 852 " --> pdb=" O ASN E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 898 Processing helix chain 'E' and resid 908 through 912 Processing helix chain 'E' and resid 922 through 931 removed outlier: 4.722A pdb=" N TYR E 928 " --> pdb=" O ILE E 924 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 929 " --> pdb=" O CYS E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 953 Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 986 through 993 Processing helix chain 'E' and resid 993 through 1007 Processing helix chain 'E' and resid 1008 through 1010 No H-bonds generated for 'chain 'E' and resid 1008 through 1010' Processing helix chain 'E' and resid 1016 through 1040 removed outlier: 3.869A pdb=" N LEU E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E1040 " --> pdb=" O LEU E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1050 through 1057 Processing helix chain 'E' and resid 1059 through 1104 removed outlier: 4.267A pdb=" N ALA E1065 " --> pdb=" O PRO E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1200 No H-bonds generated for 'chain 'E' and resid 1198 through 1200' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.909A pdb=" N ARG F 307 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 675 through 678 removed outlier: 4.527A pdb=" N ALA F 678 " --> pdb=" O GLY F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 675 through 678' Processing helix chain 'F' and resid 694 through 702 removed outlier: 3.563A pdb=" N LYS F 698 " --> pdb=" O ARG F 694 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.615A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 805 through 811 removed outlier: 3.524A pdb=" N VAL I 810 " --> pdb=" O CYS I 806 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 822 Processing helix chain 'I' and resid 824 through 854 removed outlier: 3.913A pdb=" N CYS I 828 " --> pdb=" O TYR I 824 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER I 852 " --> pdb=" O ASN I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 912 removed outlier: 4.015A pdb=" N ASP I 910 " --> pdb=" O GLN I 907 " (cutoff:3.500A) Processing helix chain 'I' and resid 922 through 931 removed outlier: 4.483A pdb=" N TYR I 928 " --> pdb=" O ILE I 924 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL I 929 " --> pdb=" O CYS I 925 " (cutoff:3.500A) Processing helix chain 'I' and resid 940 through 955 removed outlier: 3.668A pdb=" N ILE I 955 " --> pdb=" O LEU I 951 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1007 Processing helix chain 'I' and resid 1008 through 1010 No H-bonds generated for 'chain 'I' and resid 1008 through 1010' Processing helix chain 'I' and resid 1016 through 1040 removed outlier: 3.855A pdb=" N LEU I1036 " --> pdb=" O ALA I1032 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I1040 " --> pdb=" O LEU I1036 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1057 Processing helix chain 'I' and resid 1059 through 1104 removed outlier: 4.255A pdb=" N ALA I1065 " --> pdb=" O PRO I1061 " (cutoff:3.500A) Processing helix chain 'I' and resid 1198 through 1200 No H-bonds generated for 'chain 'I' and resid 1198 through 1200' Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 removed outlier: 4.050A pdb=" N ARG J 307 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 675 through 678 removed outlier: 4.540A pdb=" N ALA J 678 " --> pdb=" O GLY J 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 675 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 3.618A pdb=" N LYS J 698 " --> pdb=" O ARG J 694 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.614A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 7.303A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY B 732 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.728A pdb=" N ILE A 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.918A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 787 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.863A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.321A pdb=" N THR B 63 " --> pdb=" O TYR F 632 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.695A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.582A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.400A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AB6, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.539A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE B 186 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 237 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 188 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG B 235 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.704A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.408A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.422A pdb=" N GLU B 605 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 615 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 617 through 619 removed outlier: 4.975A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.573A pdb=" N SER C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.614A pdb=" N TYR C 98 " --> pdb=" O VAL C 100B" (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL C 100B" --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.289A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER D 49 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 719 through 724 removed outlier: 7.331A pdb=" N LEU E 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU F 722 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY F 732 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA F 737 " --> pdb=" O PRO F 730 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 777 through 782 removed outlier: 5.928A pdb=" N VAL E1150 " --> pdb=" O LYS E1174 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 787 through 796 Processing sheet with id=AD2, first strand: chain 'E' and resid 802 through 804 Processing sheet with id=AD3, first strand: chain 'E' and resid 857 through 858 Processing sheet with id=AD4, first strand: chain 'E' and resid 1202 through 1205 removed outlier: 4.261A pdb=" N CYS E1164 " --> pdb=" O VAL E1205 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS E1156 " --> pdb=" O ILE E1214 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AD6, first strand: chain 'F' and resid 63 through 64 removed outlier: 6.288A pdb=" N THR F 63 " --> pdb=" O TYR J 632 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 68 through 72 removed outlier: 3.709A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.627A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.400A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AE3, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.518A pdb=" N ALA F 146 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU F 180 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR F 242 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA F 182 " --> pdb=" O MET F 240 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET F 240 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR F 184 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE F 186 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN F 236 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU F 188 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU F 234 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.723A pdb=" N SER F 126 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AE6, first strand: chain 'F' and resid 359 through 366 removed outlier: 4.392A pdb=" N VAL F 659 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER F 365 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL F 657 " --> pdb=" O SER F 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 371 through 376 removed outlier: 4.416A pdb=" N GLU F 605 " --> pdb=" O GLY F 372 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.347A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 96 through 99 removed outlier: 4.629A pdb=" N TYR G 98 " --> pdb=" O VAL G 100B" (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL G 100B" --> pdb=" O TYR G 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.288A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER H 49 " --> pdb=" O MET H 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.325A pdb=" N LEU I 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU J 722 " --> pdb=" O LEU I 759 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 777 through 782 removed outlier: 5.916A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 787 through 796 Processing sheet with id=AF7, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'I' and resid 1202 through 1204 removed outlier: 6.809A pdb=" N CYS I1156 " --> pdb=" O ILE I1214 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AG1, first strand: chain 'J' and resid 69 through 72 removed outlier: 3.699A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AG3, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.626A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.374A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AG6, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.510A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE J 186 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS J 237 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU J 188 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG J 235 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.710A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AG9, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.403A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.427A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.362A pdb=" N SER K 44 " --> pdb=" O SER K 40 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 96 through 99 removed outlier: 4.630A pdb=" N TYR K 98 " --> pdb=" O VAL K 100B" (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL K 100B" --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.289A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2841 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: 6.43 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5924 1.32 - 1.45: 8902 1.45 - 1.58: 14513 1.58 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 29544 Sorted by residual: bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" CA PRO A1219 " pdb=" C PRO A1219 " ideal model delta sigma weight residual 1.517 1.567 -0.050 9.30e-03 1.16e+04 2.85e+01 bond pdb=" CA PRO E1219 " pdb=" C PRO E1219 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.81e+01 bond pdb=" CA PRO I1219 " pdb=" C PRO I1219 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.78e+01 bond pdb=" CA CYS I 817 " pdb=" C CYS I 817 " ideal model delta sigma weight residual 1.523 1.464 0.060 1.30e-02 5.92e+03 2.11e+01 ... (remaining 29539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 36359 2.80 - 5.59: 3292 5.59 - 8.39: 434 8.39 - 11.19: 48 11.19 - 13.99: 7 Bond angle restraints: 40140 Sorted by residual: angle pdb=" C GLN L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.66 127.44 -7.78 7.20e-01 1.93e+00 1.17e+02 angle pdb=" C GLN H 42 " pdb=" N PRO H 43 " pdb=" CA PRO H 43 " ideal model delta sigma weight residual 119.66 127.39 -7.73 7.20e-01 1.93e+00 1.15e+02 angle pdb=" C LEU B 284 " pdb=" N PRO B 285 " pdb=" CA PRO B 285 " ideal model delta sigma weight residual 119.82 129.13 -9.31 9.80e-01 1.04e+00 9.02e+01 angle pdb=" C LEU F 284 " pdb=" N PRO F 285 " pdb=" CA PRO F 285 " ideal model delta sigma weight residual 119.56 129.24 -9.68 1.02e+00 9.61e-01 9.00e+01 angle pdb=" C LEU J 284 " pdb=" N PRO J 285 " pdb=" CA PRO J 285 " ideal model delta sigma weight residual 119.56 129.19 -9.63 1.02e+00 9.61e-01 8.91e+01 ... (remaining 40135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.90: 17659 20.90 - 41.80: 427 41.80 - 62.71: 226 62.71 - 83.61: 36 83.61 - 104.51: 36 Dihedral angle restraints: 18384 sinusoidal: 7884 harmonic: 10500 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.28 -74.28 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.19 -74.19 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 166.95 -73.95 1 1.00e+01 1.00e-02 6.95e+01 ... (remaining 18381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4385 0.166 - 0.333: 210 0.333 - 0.499: 12 0.499 - 0.666: 4 0.666 - 0.832: 3 Chirality restraints: 4614 Sorted by residual: chirality pdb=" C1 NAG F1404 " pdb=" ND2 ASN F 155 " pdb=" C2 NAG F1404 " pdb=" O5 NAG F1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 66 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 619 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4611 not shown) Planarity restraints: 5175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 66 " 0.015 2.00e-02 2.50e+03 7.12e-02 6.34e+01 pdb=" CG ASN J 66 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN J 66 " 0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN J 66 " -0.126 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " -0.077 2.00e-02 2.50e+03 3.88e-02 3.76e+01 pdb=" CG TRP C 47 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.055 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1401 " 0.043 2.00e-02 2.50e+03 5.26e-02 3.46e+01 pdb=" C7 NAG B1401 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1401 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG B1401 " -0.085 2.00e-02 2.50e+03 pdb=" O7 NAG B1401 " -0.030 2.00e-02 2.50e+03 ... (remaining 5172 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 23 2.33 - 2.97: 15164 2.97 - 3.61: 38910 3.61 - 4.26: 66882 4.26 - 4.90: 107515 Nonbonded interactions: 228494 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.682 3.470 nonbonded pdb=" OH TYR E 905 " pdb=" CA PRO E 936 " model vdw 1.700 3.470 nonbonded pdb=" OH TYR I 905 " pdb=" CA PRO I 936 " model vdw 1.754 3.470 nonbonded pdb=" OH TYR I 905 " pdb=" N PRO I 936 " model vdw 1.892 3.120 nonbonded pdb=" OH TYR A 905 " pdb=" N PRO A 936 " model vdw 1.926 3.120 ... (remaining 228489 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.430 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.964 29653 Z= 0.883 Angle : 1.827 37.897 40415 Z= 1.178 Chirality : 0.087 0.832 4614 Planarity : 0.012 0.100 5133 Dihedral : 12.583 104.509 11565 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.87 % Allowed : 4.16 % Favored : 94.97 % Rotamer: Outliers : 0.16 % Allowed : 0.78 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.14), residues: 3582 helix: -0.16 (0.17), residues: 603 sheet: 0.92 (0.17), residues: 798 loop : 1.52 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 307 TYR 0.060 0.007 TYR A 909 PHE 0.032 0.005 PHE H 98 TRP 0.077 0.011 TRP C 47 HIS 0.005 0.002 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.01348 (29544) covalent geometry : angle 1.71378 (40140) SS BOND : bond 0.16315 ( 43) SS BOND : angle 7.34365 ( 86) hydrogen bonds : bond 0.20996 ( 1094) hydrogen bonds : angle 7.35372 ( 2841) Misc. bond : bond 0.01182 ( 3) link_BETA1-4 : bond 0.01405 ( 21) link_BETA1-4 : angle 3.67575 ( 63) link_NAG-ASN : bond 0.01530 ( 42) link_NAG-ASN : angle 9.54365 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 646 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 799 ILE cc_start: 0.8336 (mm) cc_final: 0.8078 (pt) REVERT: A 816 LYS cc_start: 0.8721 (tppt) cc_final: 0.8352 (tppt) REVERT: B 65 SER cc_start: 0.8039 (t) cc_final: 0.7830 (m) REVERT: B 164 PHE cc_start: 0.7471 (m-80) cc_final: 0.6896 (m-10) REVERT: B 204 PHE cc_start: 0.7757 (t80) cc_final: 0.7486 (t80) REVERT: B 621 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (m) REVERT: F 232 PHE cc_start: 0.7440 (m-80) cc_final: 0.7141 (m-80) REVERT: F 686 MET cc_start: 0.8361 (mmt) cc_final: 0.8014 (mmm) REVERT: F 696 MET cc_start: 0.7110 (mtm) cc_final: 0.6636 (ttt) REVERT: G 36 TRP cc_start: 0.8622 (m100) cc_final: 0.8397 (m-10) REVERT: H 86 TYR cc_start: 0.8377 (m-80) cc_final: 0.7960 (m-80) REVERT: I 799 ILE cc_start: 0.8442 (mm) cc_final: 0.8161 (pt) REVERT: I 932 TYR cc_start: 0.6621 (m-10) cc_final: 0.6353 (m-80) REVERT: I 988 GLN cc_start: 0.8051 (tp40) cc_final: 0.7763 (tm-30) REVERT: J 604 VAL cc_start: 0.8054 (m) cc_final: 0.7783 (m) REVERT: K 36 TRP cc_start: 0.8446 (m100) cc_final: 0.8162 (m-10) REVERT: K 82 LEU cc_start: 0.6350 (tp) cc_final: 0.6014 (tt) REVERT: L 86 TYR cc_start: 0.8461 (m-80) cc_final: 0.8218 (m-80) REVERT: L 102 THR cc_start: 0.8663 (p) cc_final: 0.8376 (m) outliers start: 5 outliers final: 0 residues processed: 650 average time/residue: 0.2079 time to fit residues: 208.1989 Evaluate side-chains 324 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 621 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN A1023 GLN A1129 ASN A1201 ASN B 208 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS E 808 GLN E1023 GLN E1129 ASN F 208 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 38 GLN H 74 ASN H 76 HIS I 808 GLN ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1129 ASN I1163 ASN I1201 ASN J 208 HIS J 346 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100219 restraints weight = 63716.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099780 restraints weight = 41011.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100834 restraints weight = 36526.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101153 restraints weight = 29791.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101390 restraints weight = 27876.783| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29653 Z= 0.173 Angle : 0.808 14.974 40415 Z= 0.418 Chirality : 0.049 0.480 4614 Planarity : 0.007 0.081 5133 Dihedral : 10.720 87.434 5263 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.96 % Favored : 95.59 % Rotamer: Outliers : 2.02 % Allowed : 6.93 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3582 helix: 1.72 (0.21), residues: 615 sheet: 0.86 (0.16), residues: 819 loop : 0.75 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 269 TYR 0.023 0.002 TYR E 905 PHE 0.021 0.002 PHE I1116 TRP 0.022 0.002 TRP G 47 HIS 0.012 0.001 HIS I1122 Details of bonding type rmsd covalent geometry : bond 0.00360 (29544) covalent geometry : angle 0.75495 (40140) SS BOND : bond 0.01149 ( 43) SS BOND : angle 2.43164 ( 86) hydrogen bonds : bond 0.07087 ( 1094) hydrogen bonds : angle 5.94441 ( 2841) Misc. bond : bond 0.00138 ( 3) link_BETA1-4 : bond 0.00568 ( 21) link_BETA1-4 : angle 2.39547 ( 63) link_NAG-ASN : bond 0.00482 ( 42) link_NAG-ASN : angle 4.57015 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 419 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.5956 (m-80) cc_final: 0.5711 (m-10) REVERT: B 181 ARG cc_start: 0.7120 (mtt-85) cc_final: 0.6909 (mtt-85) REVERT: B 621 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8582 (m) REVERT: C 43 LYS cc_start: 0.7780 (mttt) cc_final: 0.7440 (mtpp) REVERT: C 82 LEU cc_start: 0.7670 (tp) cc_final: 0.7233 (pt) REVERT: D 90 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: E 1182 ASP cc_start: 0.7037 (t0) cc_final: 0.6698 (t0) REVERT: F 318 LEU cc_start: 0.9121 (mt) cc_final: 0.8282 (mm) REVERT: F 696 MET cc_start: 0.7256 (mtm) cc_final: 0.6893 (ttt) REVERT: G 28 THR cc_start: 0.7916 (m) cc_final: 0.7669 (p) REVERT: G 36 TRP cc_start: 0.8817 (m100) cc_final: 0.8388 (m-10) REVERT: H 85 MET cc_start: 0.8679 (mmm) cc_final: 0.8269 (tpt) REVERT: H 90 GLN cc_start: 0.7730 (tt0) cc_final: 0.7378 (tt0) REVERT: H 105 GLU cc_start: 0.6570 (mp0) cc_final: 0.6348 (mp0) REVERT: I 1182 ASP cc_start: 0.7140 (t0) cc_final: 0.6860 (t0) REVERT: J 627 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: K 36 TRP cc_start: 0.8482 (m100) cc_final: 0.8086 (m-10) REVERT: K 66 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8166 (ttm-80) REVERT: K 82 LEU cc_start: 0.7828 (tp) cc_final: 0.7411 (pt) REVERT: L 85 MET cc_start: 0.8335 (tpt) cc_final: 0.8125 (mmm) REVERT: L 89 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7502 (tm-30) outliers start: 62 outliers final: 40 residues processed: 452 average time/residue: 0.1920 time to fit residues: 138.0572 Evaluate side-chains 363 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 806 CYS Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 1035 LYS Chi-restraints excluded: chain E residue 1201 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 231 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 335 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 10 optimal weight: 0.0020 chunk 178 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS B 280 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 836 HIS ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1201 ASN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.124416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094278 restraints weight = 63701.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093583 restraints weight = 39367.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094779 restraints weight = 37056.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094989 restraints weight = 30098.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095226 restraints weight = 28400.845| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 29653 Z= 0.237 Angle : 0.768 12.613 40415 Z= 0.393 Chirality : 0.048 0.402 4614 Planarity : 0.006 0.061 5133 Dihedral : 9.824 80.684 5263 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.27 % Favored : 95.28 % Rotamer: Outliers : 2.89 % Allowed : 8.94 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3582 helix: 1.84 (0.21), residues: 621 sheet: 0.70 (0.16), residues: 864 loop : 0.18 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 699 TYR 0.023 0.002 TYR B 77 PHE 0.023 0.002 PHE J 204 TRP 0.018 0.002 TRP C 47 HIS 0.016 0.002 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00551 (29544) covalent geometry : angle 0.73552 (40140) SS BOND : bond 0.00922 ( 43) SS BOND : angle 1.73365 ( 86) hydrogen bonds : bond 0.06430 ( 1094) hydrogen bonds : angle 5.65864 ( 2841) Misc. bond : bond 0.00129 ( 3) link_BETA1-4 : bond 0.00597 ( 21) link_BETA1-4 : angle 2.35233 ( 63) link_NAG-ASN : bond 0.00374 ( 42) link_NAG-ASN : angle 3.44957 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 356 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.6299 (m-80) cc_final: 0.5932 (m-10) REVERT: A 1182 ASP cc_start: 0.7551 (t0) cc_final: 0.7213 (t0) REVERT: C 62 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7801 (ptpp) REVERT: C 79 TYR cc_start: 0.7829 (m-80) cc_final: 0.7550 (m-80) REVERT: C 82 LEU cc_start: 0.7642 (tp) cc_final: 0.7427 (mm) REVERT: D 86 TYR cc_start: 0.8472 (m-80) cc_final: 0.8157 (m-80) REVERT: D 89 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 90 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: E 1084 GLN cc_start: 0.7965 (tt0) cc_final: 0.7759 (tt0) REVERT: F 696 MET cc_start: 0.7228 (mtm) cc_final: 0.6889 (ttt) REVERT: F 699 ARG cc_start: 0.6334 (ttm110) cc_final: 0.5986 (ttm110) REVERT: G 36 TRP cc_start: 0.8765 (m100) cc_final: 0.8275 (m-10) REVERT: H 102 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8671 (t) REVERT: H 105 GLU cc_start: 0.6820 (mp0) cc_final: 0.6573 (mp0) REVERT: I 913 MET cc_start: 0.5949 (ttt) cc_final: 0.5746 (ttp) REVERT: I 1182 ASP cc_start: 0.7392 (t0) cc_final: 0.6971 (t0) REVERT: J 627 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: J 696 MET cc_start: 0.7385 (mtt) cc_final: 0.7016 (mtp) REVERT: K 36 TRP cc_start: 0.8344 (m100) cc_final: 0.7926 (m-10) REVERT: L 61 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.7085 (mtp-110) REVERT: L 89 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7651 (tm-30) REVERT: L 90 GLN cc_start: 0.7964 (tt0) cc_final: 0.7475 (tt0) outliers start: 89 outliers final: 63 residues processed: 416 average time/residue: 0.1944 time to fit residues: 128.7068 Evaluate side-chains 362 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 296 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 806 CYS Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 TYR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 208 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1104 ASN A1201 ASN A1212 GLN B 208 HIS B 280 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 GLN J 91 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095967 restraints weight = 63155.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096620 restraints weight = 36831.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097296 restraints weight = 33934.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097626 restraints weight = 29078.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097818 restraints weight = 26400.955| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29653 Z= 0.131 Angle : 0.677 11.431 40415 Z= 0.341 Chirality : 0.046 0.400 4614 Planarity : 0.005 0.056 5133 Dihedral : 8.888 73.615 5262 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.13 % Favored : 95.48 % Rotamer: Outliers : 2.05 % Allowed : 10.54 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3582 helix: 2.18 (0.21), residues: 621 sheet: 0.60 (0.17), residues: 807 loop : 0.17 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 699 TYR 0.024 0.001 TYR I 777 PHE 0.028 0.001 PHE J 239 TRP 0.016 0.001 TRP C 47 HIS 0.005 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00279 (29544) covalent geometry : angle 0.64767 (40140) SS BOND : bond 0.00502 ( 43) SS BOND : angle 1.61213 ( 86) hydrogen bonds : bond 0.05307 ( 1094) hydrogen bonds : angle 5.25055 ( 2841) Misc. bond : bond 0.00082 ( 3) link_BETA1-4 : bond 0.00577 ( 21) link_BETA1-4 : angle 2.28695 ( 63) link_NAG-ASN : bond 0.00385 ( 42) link_NAG-ASN : angle 2.99328 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 340 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.6281 (m-80) cc_final: 0.5964 (m-10) REVERT: A 1182 ASP cc_start: 0.7427 (t0) cc_final: 0.7041 (t0) REVERT: B 696 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6361 (ttt) REVERT: C 43 LYS cc_start: 0.7419 (mttp) cc_final: 0.6919 (mmmm) REVERT: D 86 TYR cc_start: 0.8359 (m-80) cc_final: 0.7944 (m-80) REVERT: D 89 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 90 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: F 696 MET cc_start: 0.7210 (mtm) cc_final: 0.6954 (ttt) REVERT: F 699 ARG cc_start: 0.6350 (ttm110) cc_final: 0.6059 (ttm110) REVERT: G 36 TRP cc_start: 0.8717 (m100) cc_final: 0.8192 (m-10) REVERT: H 61 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7106 (ttm170) REVERT: H 89 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7647 (tm-30) REVERT: H 105 GLU cc_start: 0.6868 (mp0) cc_final: 0.6603 (mp0) REVERT: I 1084 GLN cc_start: 0.7941 (tt0) cc_final: 0.7711 (tt0) REVERT: I 1182 ASP cc_start: 0.7343 (t0) cc_final: 0.6878 (t0) REVERT: J 270 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: J 627 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: J 696 MET cc_start: 0.7308 (mtt) cc_final: 0.6782 (ttt) REVERT: J 699 ARG cc_start: 0.5947 (ttm110) cc_final: 0.5702 (ttm110) REVERT: K 36 TRP cc_start: 0.8049 (m100) cc_final: 0.7362 (m-10) REVERT: L 89 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7848 (tm-30) REVERT: L 90 GLN cc_start: 0.7975 (tt0) cc_final: 0.7401 (tt0) outliers start: 63 outliers final: 42 residues processed: 376 average time/residue: 0.2067 time to fit residues: 122.9133 Evaluate side-chains 354 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 806 CYS Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 93 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 225 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1085 GLN B 208 HIS B 258 GLN D 76 HIS ** E 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092542 restraints weight = 63077.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092212 restraints weight = 37567.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092919 restraints weight = 35205.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093229 restraints weight = 28686.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093577 restraints weight = 26786.472| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29653 Z= 0.207 Angle : 0.716 11.791 40415 Z= 0.359 Chirality : 0.047 0.412 4614 Planarity : 0.005 0.051 5133 Dihedral : 8.407 65.535 5262 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 2.83 % Allowed : 10.93 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3582 helix: 2.08 (0.21), residues: 618 sheet: 0.41 (0.16), residues: 906 loop : -0.05 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 699 TYR 0.025 0.001 TYR I 777 PHE 0.021 0.002 PHE J 239 TRP 0.016 0.001 TRP C 47 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00481 (29544) covalent geometry : angle 0.68739 (40140) SS BOND : bond 0.00615 ( 43) SS BOND : angle 1.60579 ( 86) hydrogen bonds : bond 0.05789 ( 1094) hydrogen bonds : angle 5.29785 ( 2841) Misc. bond : bond 0.00108 ( 3) link_BETA1-4 : bond 0.00543 ( 21) link_BETA1-4 : angle 2.34758 ( 63) link_NAG-ASN : bond 0.00345 ( 42) link_NAG-ASN : angle 3.03794 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 316 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.6661 (m-80) cc_final: 0.6313 (m-10) REVERT: B 696 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6418 (ttt) REVERT: C 43 LYS cc_start: 0.7607 (mttp) cc_final: 0.7134 (mmmm) REVERT: C 82 LEU cc_start: 0.7714 (tp) cc_final: 0.7034 (pt) REVERT: D 89 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 1182 ASP cc_start: 0.7110 (t0) cc_final: 0.6756 (t0) REVERT: F 269 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5813 (ptt90) REVERT: F 696 MET cc_start: 0.7325 (mtm) cc_final: 0.6965 (ttt) REVERT: F 699 ARG cc_start: 0.6535 (ttm110) cc_final: 0.6256 (ttm110) REVERT: G 36 TRP cc_start: 0.8740 (m100) cc_final: 0.8118 (m-10) REVERT: G 43 LYS cc_start: 0.8026 (mttt) cc_final: 0.7825 (mmmm) REVERT: H 61 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7179 (ttm170) REVERT: I 943 MET cc_start: 0.8085 (mmt) cc_final: 0.7802 (mmt) REVERT: I 1084 GLN cc_start: 0.8052 (tt0) cc_final: 0.7799 (tt0) REVERT: J 183 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: J 240 MET cc_start: 0.7489 (tpt) cc_final: 0.7286 (tpt) REVERT: J 270 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: J 627 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: J 696 MET cc_start: 0.7372 (mtt) cc_final: 0.7007 (mtp) REVERT: K 36 TRP cc_start: 0.8252 (m100) cc_final: 0.7415 (m-10) REVERT: K 43 LYS cc_start: 0.8130 (mttt) cc_final: 0.7884 (mmmm) REVERT: K 101 ASP cc_start: 0.8300 (t0) cc_final: 0.7952 (t70) REVERT: L 85 MET cc_start: 0.8209 (tpt) cc_final: 0.7818 (tpp) REVERT: L 89 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8159 (tm-30) outliers start: 87 outliers final: 62 residues processed: 370 average time/residue: 0.1966 time to fit residues: 115.2621 Evaluate side-chains 360 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 183 PHE Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 95 optimal weight: 7.9990 chunk 284 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 210 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 ASN D 6 GLN D 76 HIS E 927 GLN G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1212 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.124484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094163 restraints weight = 62664.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.094014 restraints weight = 36854.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094781 restraints weight = 33606.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095085 restraints weight = 27697.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095437 restraints weight = 25928.868| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29653 Z= 0.134 Angle : 0.672 11.169 40415 Z= 0.335 Chirality : 0.045 0.407 4614 Planarity : 0.005 0.049 5133 Dihedral : 7.885 58.153 5262 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.75 % Favored : 94.95 % Rotamer: Outliers : 2.67 % Allowed : 11.64 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3582 helix: 2.28 (0.21), residues: 618 sheet: 0.45 (0.17), residues: 876 loop : -0.10 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 699 TYR 0.028 0.001 TYR I 777 PHE 0.020 0.001 PHE J 239 TRP 0.014 0.001 TRP C 47 HIS 0.018 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00297 (29544) covalent geometry : angle 0.64423 (40140) SS BOND : bond 0.00546 ( 43) SS BOND : angle 1.63750 ( 86) hydrogen bonds : bond 0.05052 ( 1094) hydrogen bonds : angle 5.04373 ( 2841) Misc. bond : bond 0.00086 ( 3) link_BETA1-4 : bond 0.00606 ( 21) link_BETA1-4 : angle 2.30857 ( 63) link_NAG-ASN : bond 0.00435 ( 42) link_NAG-ASN : angle 2.83416 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (ttmm) REVERT: A 932 TYR cc_start: 0.6616 (m-80) cc_final: 0.6228 (m-10) REVERT: A 1182 ASP cc_start: 0.7349 (t0) cc_final: 0.6940 (t0) REVERT: B 696 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6292 (ttt) REVERT: B 699 ARG cc_start: 0.6461 (ttm110) cc_final: 0.6218 (ttm110) REVERT: C 43 LYS cc_start: 0.7601 (mttp) cc_final: 0.7105 (mmmm) REVERT: D 42 GLN cc_start: 0.7771 (mt0) cc_final: 0.7417 (mp10) REVERT: D 85 MET cc_start: 0.8512 (mmm) cc_final: 0.8061 (mmm) REVERT: D 89 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 90 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: F 269 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5688 (ptt90) REVERT: F 696 MET cc_start: 0.7266 (mtm) cc_final: 0.6886 (ttt) REVERT: F 699 ARG cc_start: 0.6416 (ttm110) cc_final: 0.6168 (ttm110) REVERT: G 36 TRP cc_start: 0.8688 (m100) cc_final: 0.7989 (m-10) REVERT: G 43 LYS cc_start: 0.7924 (mttt) cc_final: 0.7266 (mmmm) REVERT: H 85 MET cc_start: 0.8587 (mmm) cc_final: 0.8067 (mmm) REVERT: I 757 MET cc_start: 0.8180 (mmt) cc_final: 0.7728 (mmt) REVERT: I 943 MET cc_start: 0.8012 (mmt) cc_final: 0.7763 (mmt) REVERT: I 1182 ASP cc_start: 0.7149 (t0) cc_final: 0.6806 (t0) REVERT: J 183 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6733 (m-10) REVERT: J 240 MET cc_start: 0.7533 (tpt) cc_final: 0.7311 (tpt) REVERT: J 270 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: J 627 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: J 686 MET cc_start: 0.8190 (mmp) cc_final: 0.7849 (mmm) REVERT: J 696 MET cc_start: 0.7258 (mtt) cc_final: 0.6632 (ttt) REVERT: K 36 TRP cc_start: 0.8177 (m100) cc_final: 0.7359 (m-10) REVERT: K 82 LEU cc_start: 0.6140 (tp) cc_final: 0.5807 (tt) REVERT: K 101 ASP cc_start: 0.8302 (t0) cc_final: 0.7947 (t70) REVERT: L 89 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7992 (tm-30) REVERT: L 90 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7183 (pp30) outliers start: 82 outliers final: 55 residues processed: 376 average time/residue: 0.1879 time to fit residues: 113.5041 Evaluate side-chains 367 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 183 PHE Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 264 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094184 restraints weight = 62925.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.094198 restraints weight = 36686.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094735 restraints weight = 33468.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095015 restraints weight = 28518.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095422 restraints weight = 26412.251| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29653 Z= 0.134 Angle : 0.656 11.032 40415 Z= 0.326 Chirality : 0.045 0.421 4614 Planarity : 0.005 0.055 5133 Dihedral : 7.473 57.905 5262 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.14 % Favored : 94.58 % Rotamer: Outliers : 2.93 % Allowed : 12.00 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3582 helix: 2.36 (0.21), residues: 618 sheet: 0.59 (0.17), residues: 846 loop : -0.19 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 699 TYR 0.027 0.001 TYR I 777 PHE 0.021 0.001 PHE B 204 TRP 0.014 0.001 TRP C 47 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00299 (29544) covalent geometry : angle 0.63125 (40140) SS BOND : bond 0.00478 ( 43) SS BOND : angle 1.43172 ( 86) hydrogen bonds : bond 0.04823 ( 1094) hydrogen bonds : angle 4.92520 ( 2841) Misc. bond : bond 0.00090 ( 3) link_BETA1-4 : bond 0.00622 ( 21) link_BETA1-4 : angle 2.26973 ( 63) link_NAG-ASN : bond 0.00481 ( 42) link_NAG-ASN : angle 2.69436 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 328 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8255 (ttmm) REVERT: A 932 TYR cc_start: 0.6770 (m-80) cc_final: 0.6440 (m-80) REVERT: A 1182 ASP cc_start: 0.7281 (t0) cc_final: 0.6856 (t0) REVERT: B 696 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6348 (ttt) REVERT: C 43 LYS cc_start: 0.7636 (mttp) cc_final: 0.7050 (mmmm) REVERT: D 89 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7822 (tm-30) REVERT: D 90 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: E 1182 ASP cc_start: 0.6893 (t0) cc_final: 0.6649 (t0) REVERT: F 240 MET cc_start: 0.7614 (mmm) cc_final: 0.7313 (mmm) REVERT: F 269 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5779 (ptt90) REVERT: F 686 MET cc_start: 0.8216 (mmp) cc_final: 0.7890 (mmm) REVERT: F 696 MET cc_start: 0.7254 (mtm) cc_final: 0.6857 (ttt) REVERT: F 699 ARG cc_start: 0.6441 (ttm110) cc_final: 0.6173 (ttm110) REVERT: G 36 TRP cc_start: 0.8700 (m100) cc_final: 0.8337 (m100) REVERT: G 43 LYS cc_start: 0.7946 (mttt) cc_final: 0.7174 (mmmm) REVERT: H 61 ARG cc_start: 0.7570 (ttm170) cc_final: 0.7315 (ttm170) REVERT: H 85 MET cc_start: 0.8558 (mmm) cc_final: 0.8073 (mmm) REVERT: I 757 MET cc_start: 0.8138 (mmt) cc_final: 0.7676 (mmt) REVERT: I 875 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6704 (mm-30) REVERT: I 943 MET cc_start: 0.8008 (mmt) cc_final: 0.7749 (mmt) REVERT: I 1084 GLN cc_start: 0.8023 (tt0) cc_final: 0.7803 (tt0) REVERT: I 1182 ASP cc_start: 0.7293 (t0) cc_final: 0.6956 (t0) REVERT: J 270 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: J 627 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: J 686 MET cc_start: 0.8084 (mmp) cc_final: 0.7707 (mmm) REVERT: J 696 MET cc_start: 0.7192 (mtt) cc_final: 0.6590 (ttt) REVERT: K 6 GLN cc_start: 0.7845 (mt0) cc_final: 0.7643 (mt0) REVERT: K 36 TRP cc_start: 0.8161 (m100) cc_final: 0.7313 (m-10) REVERT: K 82 LEU cc_start: 0.6151 (tp) cc_final: 0.5781 (tt) REVERT: L 61 ARG cc_start: 0.7205 (mtp-110) cc_final: 0.6830 (ttp80) REVERT: L 90 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7280 (pp30) outliers start: 90 outliers final: 69 residues processed: 390 average time/residue: 0.1824 time to fit residues: 114.3436 Evaluate side-chains 383 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 347 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS E1146 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.121074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091292 restraints weight = 63260.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.090372 restraints weight = 38481.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091870 restraints weight = 39826.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091955 restraints weight = 29697.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092336 restraints weight = 27528.667| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 29653 Z= 0.299 Angle : 0.787 11.949 40415 Z= 0.394 Chirality : 0.048 0.403 4614 Planarity : 0.005 0.051 5133 Dihedral : 7.761 59.862 5262 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.81 % Favored : 93.91 % Rotamer: Outliers : 3.45 % Allowed : 11.84 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3582 helix: 2.01 (0.21), residues: 618 sheet: 0.45 (0.18), residues: 849 loop : -0.49 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 66 TYR 0.027 0.002 TYR I 777 PHE 0.025 0.002 PHE J 239 TRP 0.014 0.002 TRP C 47 HIS 0.006 0.002 HIS E1146 Details of bonding type rmsd covalent geometry : bond 0.00702 (29544) covalent geometry : angle 0.75912 (40140) SS BOND : bond 0.00740 ( 43) SS BOND : angle 1.91266 ( 86) hydrogen bonds : bond 0.06177 ( 1094) hydrogen bonds : angle 5.33162 ( 2841) Misc. bond : bond 0.00123 ( 3) link_BETA1-4 : bond 0.00712 ( 21) link_BETA1-4 : angle 2.38949 ( 63) link_NAG-ASN : bond 0.00486 ( 42) link_NAG-ASN : angle 3.08268 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 315 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8413 (ttmm) REVERT: A 932 TYR cc_start: 0.7065 (m-80) cc_final: 0.6683 (m-80) REVERT: A 1182 ASP cc_start: 0.7541 (t0) cc_final: 0.7080 (t70) REVERT: C 43 LYS cc_start: 0.7818 (mttp) cc_final: 0.7319 (mmmm) REVERT: D 42 GLN cc_start: 0.7786 (mt0) cc_final: 0.7423 (mp10) REVERT: D 85 MET cc_start: 0.8577 (mmm) cc_final: 0.8162 (mmm) REVERT: D 89 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7948 (tm-30) REVERT: F 240 MET cc_start: 0.7765 (mmm) cc_final: 0.7558 (mmm) REVERT: F 269 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5910 (ptt90) REVERT: F 696 MET cc_start: 0.7261 (mtm) cc_final: 0.6872 (ttt) REVERT: G 36 TRP cc_start: 0.8733 (m100) cc_final: 0.8429 (m100) REVERT: H 61 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7423 (ttm170) REVERT: H 85 MET cc_start: 0.8587 (mmm) cc_final: 0.8362 (tpt) REVERT: I 757 MET cc_start: 0.8082 (mmt) cc_final: 0.7652 (mmt) REVERT: I 924 ILE cc_start: 0.5509 (OUTLIER) cc_final: 0.5156 (pt) REVERT: I 943 MET cc_start: 0.8124 (mmt) cc_final: 0.7835 (mmt) REVERT: I 1084 GLN cc_start: 0.8223 (tt0) cc_final: 0.7997 (tt0) REVERT: J 240 MET cc_start: 0.7616 (mmm) cc_final: 0.6839 (mmm) REVERT: J 270 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: J 627 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: J 696 MET cc_start: 0.7277 (mtt) cc_final: 0.6871 (mtp) REVERT: K 5 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7811 (tm-30) REVERT: K 36 TRP cc_start: 0.8276 (m100) cc_final: 0.7363 (m-10) REVERT: L 61 ARG cc_start: 0.7268 (mtp-110) cc_final: 0.6936 (ttp80) REVERT: L 85 MET cc_start: 0.8397 (tpt) cc_final: 0.7938 (tpp) REVERT: L 86 TYR cc_start: 0.8575 (m-80) cc_final: 0.8346 (m-80) REVERT: L 90 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7677 (pp30) outliers start: 106 outliers final: 84 residues processed: 396 average time/residue: 0.1828 time to fit residues: 116.1434 Evaluate side-chains 392 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 302 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 932 TYR Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain E residue 1214 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 862 ILE Chi-restraints excluded: chain I residue 924 ILE Chi-restraints excluded: chain I residue 925 CYS Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 99 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092902 restraints weight = 62812.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092802 restraints weight = 36824.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093587 restraints weight = 33073.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093892 restraints weight = 27657.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094220 restraints weight = 25848.508| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29653 Z= 0.138 Angle : 0.697 11.895 40415 Z= 0.344 Chirality : 0.046 0.413 4614 Planarity : 0.005 0.059 5133 Dihedral : 7.401 58.226 5262 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.22 % Favored : 94.56 % Rotamer: Outliers : 2.67 % Allowed : 13.14 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3582 helix: 2.28 (0.21), residues: 618 sheet: 0.52 (0.18), residues: 855 loop : -0.44 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 66 TYR 0.025 0.001 TYR I 777 PHE 0.020 0.001 PHE B 204 TRP 0.013 0.001 TRP C 47 HIS 0.003 0.001 HIS J 208 Details of bonding type rmsd covalent geometry : bond 0.00305 (29544) covalent geometry : angle 0.67091 (40140) SS BOND : bond 0.00471 ( 43) SS BOND : angle 1.44415 ( 86) hydrogen bonds : bond 0.05089 ( 1094) hydrogen bonds : angle 4.97848 ( 2841) Misc. bond : bond 0.00086 ( 3) link_BETA1-4 : bond 0.00520 ( 21) link_BETA1-4 : angle 2.22880 ( 63) link_NAG-ASN : bond 0.00372 ( 42) link_NAG-ASN : angle 2.93119 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 324 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8279 (ttmm) REVERT: A 932 TYR cc_start: 0.6787 (m-80) cc_final: 0.6580 (m-10) REVERT: A 1182 ASP cc_start: 0.7420 (t0) cc_final: 0.6957 (t0) REVERT: A 1222 LEU cc_start: 0.7761 (tp) cc_final: 0.7561 (mt) REVERT: B 696 MET cc_start: 0.7035 (mtt) cc_final: 0.6341 (ttt) REVERT: C 43 LYS cc_start: 0.7895 (mttp) cc_final: 0.7289 (mmmm) REVERT: D 42 GLN cc_start: 0.7723 (mt0) cc_final: 0.7322 (pm20) REVERT: D 61 ARG cc_start: 0.7165 (mtp-110) cc_final: 0.6725 (mmt180) REVERT: D 89 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 90 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: F 161 MET cc_start: 0.4935 (mmm) cc_final: 0.4346 (mmm) REVERT: F 269 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5826 (ptt90) REVERT: F 352 GLU cc_start: 0.7655 (mp0) cc_final: 0.7359 (mp0) REVERT: F 696 MET cc_start: 0.7225 (mtm) cc_final: 0.6788 (ttt) REVERT: F 699 ARG cc_start: 0.6540 (ttm110) cc_final: 0.6211 (ttm110) REVERT: G 36 TRP cc_start: 0.8699 (m100) cc_final: 0.8382 (m100) REVERT: G 43 LYS cc_start: 0.7756 (mmtt) cc_final: 0.6976 (mmmm) REVERT: H 42 GLN cc_start: 0.7883 (mt0) cc_final: 0.7457 (pm20) REVERT: H 85 MET cc_start: 0.8556 (mmm) cc_final: 0.8084 (mmm) REVERT: I 757 MET cc_start: 0.8078 (mmt) cc_final: 0.7624 (mmt) REVERT: I 943 MET cc_start: 0.8062 (mmt) cc_final: 0.7761 (mmt) REVERT: I 1050 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8141 (p) REVERT: J 240 MET cc_start: 0.7604 (mmm) cc_final: 0.7144 (mmm) REVERT: J 270 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: J 627 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: J 696 MET cc_start: 0.7215 (mtt) cc_final: 0.6857 (mtp) REVERT: K 36 TRP cc_start: 0.8242 (m100) cc_final: 0.7471 (m-10) REVERT: L 61 ARG cc_start: 0.7322 (mtp-110) cc_final: 0.6979 (ttp80) REVERT: L 85 MET cc_start: 0.8457 (tpt) cc_final: 0.8048 (tpt) REVERT: L 89 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7979 (tm-30) outliers start: 82 outliers final: 65 residues processed: 377 average time/residue: 0.1883 time to fit residues: 114.6570 Evaluate side-chains 377 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 306 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 1050 SER Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 709 THR Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 157 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092560 restraints weight = 62571.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092325 restraints weight = 38459.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093265 restraints weight = 34543.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093483 restraints weight = 28398.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093776 restraints weight = 26690.283| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 29653 Z= 0.170 Angle : 0.712 14.971 40415 Z= 0.352 Chirality : 0.046 0.415 4614 Planarity : 0.005 0.064 5133 Dihedral : 7.232 58.488 5262 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.58 % Favored : 94.19 % Rotamer: Outliers : 2.60 % Allowed : 13.40 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3582 helix: 2.26 (0.21), residues: 618 sheet: 0.62 (0.18), residues: 816 loop : -0.51 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 66 TYR 0.024 0.001 TYR I 777 PHE 0.018 0.001 PHE J 239 TRP 0.011 0.001 TRP C 47 HIS 0.004 0.001 HIS A1146 Details of bonding type rmsd covalent geometry : bond 0.00395 (29544) covalent geometry : angle 0.68228 (40140) SS BOND : bond 0.00558 ( 43) SS BOND : angle 2.16610 ( 86) hydrogen bonds : bond 0.05166 ( 1094) hydrogen bonds : angle 4.99208 ( 2841) Misc. bond : bond 0.00083 ( 3) link_BETA1-4 : bond 0.00649 ( 21) link_BETA1-4 : angle 2.17025 ( 63) link_NAG-ASN : bond 0.00394 ( 42) link_NAG-ASN : angle 2.93398 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 310 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8304 (ttmm) REVERT: A 932 TYR cc_start: 0.6827 (m-80) cc_final: 0.6547 (m-10) REVERT: A 1182 ASP cc_start: 0.7457 (t0) cc_final: 0.7024 (t0) REVERT: A 1222 LEU cc_start: 0.7750 (tp) cc_final: 0.7532 (mt) REVERT: B 696 MET cc_start: 0.7055 (mtt) cc_final: 0.6362 (ttt) REVERT: C 43 LYS cc_start: 0.7942 (mttp) cc_final: 0.7403 (mmmm) REVERT: D 42 GLN cc_start: 0.7750 (mt0) cc_final: 0.7385 (pm20) REVERT: D 61 ARG cc_start: 0.7062 (mtp-110) cc_final: 0.6763 (mmt180) REVERT: D 85 MET cc_start: 0.8557 (mmm) cc_final: 0.8185 (mmm) REVERT: D 89 GLN cc_start: 0.8251 (tm-30) cc_final: 0.8001 (tm-30) REVERT: F 161 MET cc_start: 0.5099 (mmm) cc_final: 0.4345 (mmm) REVERT: F 240 MET cc_start: 0.7990 (mmm) cc_final: 0.7724 (mmm) REVERT: F 269 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.5898 (ptt90) REVERT: F 352 GLU cc_start: 0.7670 (mp0) cc_final: 0.7350 (mp0) REVERT: F 696 MET cc_start: 0.7221 (mtm) cc_final: 0.6817 (ttt) REVERT: F 699 ARG cc_start: 0.6566 (ttm110) cc_final: 0.6238 (ttm110) REVERT: G 36 TRP cc_start: 0.8701 (m100) cc_final: 0.8368 (m100) REVERT: G 43 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7009 (mmmm) REVERT: H 42 GLN cc_start: 0.7875 (mt0) cc_final: 0.7483 (pm20) REVERT: H 61 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7076 (ttm170) REVERT: H 85 MET cc_start: 0.8504 (mmm) cc_final: 0.8259 (mmm) REVERT: I 757 MET cc_start: 0.8093 (mmt) cc_final: 0.7661 (mmt) REVERT: I 924 ILE cc_start: 0.5250 (OUTLIER) cc_final: 0.4977 (pt) REVERT: I 943 MET cc_start: 0.8080 (mmt) cc_final: 0.7786 (mmt) REVERT: J 240 MET cc_start: 0.7731 (mmm) cc_final: 0.7300 (mmm) REVERT: J 270 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: J 627 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: J 696 MET cc_start: 0.7186 (mtt) cc_final: 0.6798 (mtp) REVERT: K 36 TRP cc_start: 0.8254 (m100) cc_final: 0.7444 (m-10) REVERT: L 61 ARG cc_start: 0.7230 (mtp-110) cc_final: 0.6850 (mmt180) REVERT: L 89 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8199 (tm-30) outliers start: 80 outliers final: 69 residues processed: 366 average time/residue: 0.1876 time to fit residues: 111.0062 Evaluate side-chains 378 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 304 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 924 ILE Chi-restraints excluded: chain I residue 925 CYS Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 709 THR Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 322 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 314 optimal weight: 0.5980 chunk 317 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 ASN D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093368 restraints weight = 63259.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.093000 restraints weight = 37279.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094002 restraints weight = 34125.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094185 restraints weight = 29222.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094439 restraints weight = 27138.798| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29653 Z= 0.146 Angle : 0.687 12.124 40415 Z= 0.340 Chirality : 0.045 0.414 4614 Planarity : 0.005 0.065 5133 Dihedral : 7.029 57.904 5262 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.53 % Favored : 94.25 % Rotamer: Outliers : 2.60 % Allowed : 13.46 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3582 helix: 2.32 (0.21), residues: 618 sheet: 0.62 (0.18), residues: 816 loop : -0.52 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 66 TYR 0.023 0.001 TYR I 777 PHE 0.020 0.001 PHE B 228 TRP 0.010 0.001 TRP G 47 HIS 0.003 0.001 HIS A1146 Details of bonding type rmsd covalent geometry : bond 0.00333 (29544) covalent geometry : angle 0.66012 (40140) SS BOND : bond 0.00457 ( 43) SS BOND : angle 1.84955 ( 86) hydrogen bonds : bond 0.04882 ( 1094) hydrogen bonds : angle 4.88939 ( 2841) Misc. bond : bond 0.00093 ( 3) link_BETA1-4 : bond 0.00585 ( 21) link_BETA1-4 : angle 2.09220 ( 63) link_NAG-ASN : bond 0.00373 ( 42) link_NAG-ASN : angle 2.80382 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4554.57 seconds wall clock time: 79 minutes 53.34 seconds (4793.34 seconds total)