Starting phenix.real_space_refine on Thu Mar 21 01:46:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9i_8784/03_2024/5w9i_8784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9i_8784/03_2024/5w9i_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9i_8784/03_2024/5w9i_8784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9i_8784/03_2024/5w9i_8784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9i_8784/03_2024/5w9i_8784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9i_8784/03_2024/5w9i_8784.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "I TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 188": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 15.80, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 11.82 Conformation dependent library (CDL) restraints added in 5.1 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: 3.53 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: 11.52 Time building geometry restraints manager: 12.76 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: 96.21 - 104.77: 551 104.77 - 113.32: 15486 113.32 - 121.88: 18191 121.88 - 130.43: 5820 130.43 - 138.99: 92 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 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: 5.060 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: 0.000 Extract box with map and model: 7.420 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 77.820 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.850 ------------------------------------------------------------------------------- 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 : 0.013 0.115 29544 Z= 0.877 Angle : 1.714 13.987 40140 Z= 1.156 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 : 4.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.077 0.011 TRP C 47 HIS 0.005 0.002 HIS B 681 PHE 0.032 0.005 PHE H 98 TYR 0.060 0.007 TYR A 909 ARG 0.005 0.001 ARG J 307 *********************** 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 fitting. rotamer outliers: 5 poor density : 646 time to evaluate : 2.719 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: 0.4346 time to fit residues: 431.0246 Evaluate side-chains 324 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 3.311 ------------------------------------------------------------------------------- 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 301 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29544 Z= 0.218 Angle : 0.731 9.848 40140 Z= 0.390 Chirality : 0.049 0.457 4614 Planarity : 0.007 0.079 5133 Dihedral : 10.729 86.947 5263 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.02 % Favored : 95.51 % Rotamer: Outliers : 2.21 % Allowed : 6.89 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.14), residues: 3582 helix: 1.76 (0.21), residues: 615 sheet: 0.86 (0.17), residues: 777 loop : 0.71 (0.14), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 47 HIS 0.010 0.001 HIS I1122 PHE 0.021 0.002 PHE F 254 TYR 0.022 0.001 TYR F 77 ARG 0.006 0.000 ARG J 269 *********************** 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 489 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 421 time to evaluate : 3.500 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 913 MET cc_start: 0.7394 (mmm) cc_final: 0.6782 (ttp) REVERT: A 932 TYR cc_start: 0.5868 (m-80) cc_final: 0.5524 (m-10) REVERT: B 621 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8686 (m) REVERT: B 717 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6896 (mm) REVERT: C 43 LYS cc_start: 0.7604 (mttt) cc_final: 0.7399 (mtpp) REVERT: C 79 TYR cc_start: 0.7701 (m-80) cc_final: 0.7500 (m-80) REVERT: D 90 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: F 183 PHE cc_start: 0.6956 (m-80) cc_final: 0.6592 (m-80) REVERT: F 269 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6285 (ptt90) REVERT: F 696 MET cc_start: 0.7126 (mtm) cc_final: 0.6737 (ttt) REVERT: G 28 THR cc_start: 0.8001 (m) cc_final: 0.7672 (p) REVERT: G 36 TRP cc_start: 0.8662 (m100) cc_final: 0.8440 (m-10) REVERT: H 90 GLN cc_start: 0.7638 (tt0) cc_final: 0.7286 (tt0) REVERT: I 913 MET cc_start: 0.7429 (tpp) cc_final: 0.6976 (ttt) REVERT: I 1050 SER cc_start: 0.8397 (t) cc_final: 0.8109 (p) REVERT: I 1182 ASP cc_start: 0.7534 (t0) cc_final: 0.7300 (t0) REVERT: J 627 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: K 36 TRP cc_start: 0.8346 (m100) cc_final: 0.8127 (m-10) REVERT: L 89 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8088 (tm-30) outliers start: 68 outliers final: 41 residues processed: 459 average time/residue: 0.4136 time to fit residues: 300.1149 Evaluate side-chains 360 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 314 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 872 THR 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 621 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 717 LEU 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 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 350 SER Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain G residue 20 ILE 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 I residue 1185 SER 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 Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 324 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 289 optimal weight: 0.0030 chunk 322 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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** A1212 GLN B 208 HIS B 280 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 208 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1201 ASN I1212 GLN J 98 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29544 Z= 0.194 Angle : 0.649 9.540 40140 Z= 0.340 Chirality : 0.046 0.397 4614 Planarity : 0.005 0.059 5133 Dihedral : 9.708 80.243 5263 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.24 % Favored : 95.31 % Rotamer: Outliers : 2.31 % Allowed : 8.98 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3582 helix: 2.16 (0.21), residues: 621 sheet: 0.77 (0.17), residues: 774 loop : 0.44 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.009 0.001 HIS B 208 PHE 0.027 0.001 PHE J 204 TYR 0.016 0.001 TYR E1141 ARG 0.005 0.000 ARG J 699 *********************** 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 442 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 371 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 913 MET cc_start: 0.7389 (mmm) cc_final: 0.6828 (ttp) REVERT: D 70 ASP cc_start: 0.8340 (p0) cc_final: 0.8124 (p0) REVERT: D 89 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8021 (tm-30) REVERT: D 90 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: E 944 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7507 (mt-10) REVERT: F 696 MET cc_start: 0.6933 (mtm) cc_final: 0.6629 (ttt) REVERT: G 36 TRP cc_start: 0.8548 (m100) cc_final: 0.8279 (m-10) REVERT: G 66 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7646 (mtp180) REVERT: I 913 MET cc_start: 0.6463 (tpp) cc_final: 0.6029 (ttt) REVERT: I 1084 GLN cc_start: 0.8101 (tt0) cc_final: 0.7777 (tt0) REVERT: J 627 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: K 36 TRP cc_start: 0.8104 (m100) cc_final: 0.7669 (m-10) REVERT: L 46 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8049 (tp) REVERT: L 89 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7975 (tm-30) outliers start: 71 outliers final: 48 residues processed: 415 average time/residue: 0.4006 time to fit residues: 265.5232 Evaluate side-chains 361 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 310 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 954 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 208 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain C residue 107 THR 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 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 1168 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain F residue 135 SER 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 651 LEU 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 110 THR Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 136 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 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 TYR Chi-restraints excluded: chain L residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 325 optimal weight: 8.9990 chunk 345 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 308 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS A1085 GLN A1146 HIS A1201 ASN B 208 HIS B 258 GLN C 61 GLN D 76 HIS E 836 HIS E 927 GLN E1212 GLN F 111 GLN F 208 HIS G 39 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 836 HIS J 91 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29544 Z= 0.296 Angle : 0.677 11.127 40140 Z= 0.349 Chirality : 0.046 0.403 4614 Planarity : 0.005 0.054 5133 Dihedral : 9.079 73.638 5262 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.72 % Favored : 94.89 % Rotamer: Outliers : 3.19 % Allowed : 9.76 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3582 helix: 2.23 (0.21), residues: 621 sheet: 0.76 (0.17), residues: 843 loop : 0.19 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.019 0.002 HIS B 208 PHE 0.028 0.002 PHE J 239 TYR 0.017 0.001 TYR A1141 ARG 0.006 0.000 ARG J 235 *********************** 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 423 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 325 time to evaluate : 3.272 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: B 696 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6236 (ttt) REVERT: C 43 LYS cc_start: 0.7793 (mttt) cc_final: 0.7584 (mmtp) REVERT: C 82 LEU cc_start: 0.7634 (tp) cc_final: 0.7375 (mm) REVERT: D 89 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 90 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: F 696 MET cc_start: 0.7137 (mtm) cc_final: 0.6783 (ttt) REVERT: F 699 ARG cc_start: 0.6325 (ttm110) cc_final: 0.6039 (ttm110) REVERT: G 36 TRP cc_start: 0.8583 (m100) cc_final: 0.8168 (m-10) REVERT: I 913 MET cc_start: 0.6555 (tpp) cc_final: 0.6078 (ttt) REVERT: I 1084 GLN cc_start: 0.8172 (tt0) cc_final: 0.7885 (tt0) REVERT: J 270 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: J 627 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: J 696 MET cc_start: 0.7349 (mtt) cc_final: 0.6512 (ttt) REVERT: J 699 ARG cc_start: 0.6011 (ttm110) cc_final: 0.5735 (ttm110) REVERT: K 34 ILE cc_start: 0.9510 (mm) cc_final: 0.9203 (mt) REVERT: K 36 TRP cc_start: 0.8306 (m100) cc_final: 0.8104 (m-10) outliers start: 98 outliers final: 76 residues processed: 394 average time/residue: 0.4416 time to fit residues: 274.6143 Evaluate side-chains 372 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 292 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1034 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 136 THR 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 625 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain C residue 82 LEU 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 46 LEU 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 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 E residue 1168 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 125 ASN 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 717 LEU 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 107 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 1034 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 136 THR 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 604 VAL 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 28 THR 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 47 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 309 optimal weight: 0.0040 chunk 87 optimal weight: 0.6980 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1104 ASN A1201 ASN B 98 GLN B 208 HIS B 280 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS F 208 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29544 Z= 0.251 Angle : 0.641 9.420 40140 Z= 0.328 Chirality : 0.045 0.408 4614 Planarity : 0.005 0.052 5133 Dihedral : 8.418 66.817 5262 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.84 % Rotamer: Outliers : 3.35 % Allowed : 10.47 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3582 helix: 2.29 (0.21), residues: 621 sheet: 0.67 (0.17), residues: 864 loop : 0.08 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.011 0.001 HIS B 208 PHE 0.021 0.001 PHE J 239 TYR 0.023 0.001 TYR I 777 ARG 0.005 0.000 ARG B 699 *********************** 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 425 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 322 time to evaluate : 2.814 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: B 696 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6145 (ttt) REVERT: B 699 ARG cc_start: 0.6197 (ttm110) cc_final: 0.5969 (ttm110) REVERT: C 43 LYS cc_start: 0.7878 (mttt) cc_final: 0.7490 (mtpp) REVERT: C 82 LEU cc_start: 0.7580 (tp) cc_final: 0.7295 (mm) REVERT: D 6 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: D 89 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8145 (tm-30) REVERT: D 90 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: F 696 MET cc_start: 0.7235 (mtm) cc_final: 0.6825 (ttt) REVERT: G 36 TRP cc_start: 0.8580 (m100) cc_final: 0.8146 (m-10) REVERT: I 913 MET cc_start: 0.6495 (tpp) cc_final: 0.6270 (ttt) REVERT: I 1084 GLN cc_start: 0.8214 (tt0) cc_final: 0.7915 (tt0) REVERT: J 270 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: J 304 GLN cc_start: 0.6579 (tp40) cc_final: 0.6024 (tm-30) REVERT: J 627 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8412 (pt0) REVERT: J 696 MET cc_start: 0.7357 (mtt) cc_final: 0.6586 (ttt) REVERT: K 36 TRP cc_start: 0.8363 (m100) cc_final: 0.8160 (m-10) REVERT: K 82 LEU cc_start: 0.5952 (tp) cc_final: 0.5599 (tt) REVERT: L 76 HIS cc_start: 0.6740 (m-70) cc_final: 0.6524 (m-70) outliers start: 103 outliers final: 78 residues processed: 395 average time/residue: 0.3957 time to fit residues: 248.3235 Evaluate side-chains 381 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 298 time to evaluate : 3.118 ------------------------------------------------------------------------------- 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 862 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 136 THR 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 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 86 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 THR 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 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 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR 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 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 52 THR 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 H residue 47 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 90 GLN 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 852 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 872 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 136 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 604 VAL 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 28 THR 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 20 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 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 345 optimal weight: 0.3980 chunk 286 optimal weight: 10.0000 chunk 159 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 overall best weight: 2.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 ASN B 208 HIS D 76 HIS F 208 HIS G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29544 Z= 0.248 Angle : 0.646 10.249 40140 Z= 0.328 Chirality : 0.045 0.415 4614 Planarity : 0.005 0.051 5133 Dihedral : 7.879 58.033 5262 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.05 % Favored : 94.64 % Rotamer: Outliers : 3.58 % Allowed : 10.80 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3582 helix: 2.34 (0.21), residues: 618 sheet: 0.69 (0.17), residues: 870 loop : -0.03 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.013 0.001 HIS F 208 PHE 0.018 0.001 PHE J 239 TYR 0.022 0.001 TYR I 777 ARG 0.007 0.000 ARG F 699 *********************** 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 421 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 311 time to evaluate : 2.932 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 1116 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8333 (t80) REVERT: B 696 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6172 (ttt) REVERT: D 90 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: F 269 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5730 (ptt90) REVERT: F 686 MET cc_start: 0.8148 (mmp) cc_final: 0.7915 (mmm) REVERT: F 696 MET cc_start: 0.7216 (mtm) cc_final: 0.6808 (ttt) REVERT: F 699 ARG cc_start: 0.6324 (ttm110) cc_final: 0.5992 (ttm110) REVERT: G 36 TRP cc_start: 0.8568 (m100) cc_final: 0.8047 (m-10) REVERT: I 913 MET cc_start: 0.6538 (tpp) cc_final: 0.6169 (ttt) REVERT: I 943 MET cc_start: 0.8279 (mmm) cc_final: 0.7975 (mmt) REVERT: I 1116 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8629 (t80) REVERT: J 270 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: J 304 GLN cc_start: 0.6609 (tp40) cc_final: 0.6017 (tm-30) REVERT: J 627 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: J 696 MET cc_start: 0.7413 (mtt) cc_final: 0.6629 (ttt) REVERT: K 34 ILE cc_start: 0.9518 (mm) cc_final: 0.9228 (mm) REVERT: K 36 TRP cc_start: 0.8393 (m100) cc_final: 0.8160 (m-10) REVERT: K 82 LEU cc_start: 0.6053 (tp) cc_final: 0.5682 (tt) REVERT: L 76 HIS cc_start: 0.6773 (m-70) cc_final: 0.6536 (m-70) outliers start: 110 outliers final: 87 residues processed: 395 average time/residue: 0.3887 time to fit residues: 245.4959 Evaluate side-chains 389 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 295 time to evaluate : 3.151 ------------------------------------------------------------------------------- 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 872 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1116 PHE 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 136 THR Chi-restraints excluded: chain B residue 183 PHE 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 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 86 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 46 LEU 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 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 125 ASN 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 140 ILE Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 269 ARG 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 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 52 THR 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 H residue 47 LEU 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 852 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 1034 SER Chi-restraints excluded: chain I residue 1116 PHE 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 I residue 1214 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 136 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 604 VAL 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 28 THR 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 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 192 optimal weight: 0.0070 chunk 344 optimal weight: 20.0000 chunk 215 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS F 208 HIS ** H 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29544 Z= 0.251 Angle : 0.652 10.312 40140 Z= 0.331 Chirality : 0.045 0.414 4614 Planarity : 0.005 0.051 5133 Dihedral : 7.653 57.831 5262 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.08 % Favored : 94.58 % Rotamer: Outliers : 3.87 % Allowed : 11.35 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3582 helix: 2.36 (0.21), residues: 618 sheet: 0.66 (0.17), residues: 831 loop : -0.14 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.019 0.001 HIS F 208 PHE 0.018 0.001 PHE B 239 TYR 0.024 0.001 TYR I 777 ARG 0.007 0.000 ARG J 699 *********************** 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 438 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 319 time to evaluate : 3.075 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: 0.8523 (OUTLIER) cc_final: 0.8263 (ttmm) REVERT: A 1116 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8439 (t80) REVERT: B 240 MET cc_start: 0.8282 (tpp) cc_final: 0.7850 (tpt) REVERT: B 696 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6176 (ttt) REVERT: C 43 LYS cc_start: 0.7464 (mttp) cc_final: 0.7042 (mmmm) REVERT: D 42 GLN cc_start: 0.6887 (mp10) cc_final: 0.6617 (pm20) REVERT: D 89 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 792 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: F 269 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5715 (ptt90) REVERT: F 686 MET cc_start: 0.8202 (mmp) cc_final: 0.7973 (mmm) REVERT: F 696 MET cc_start: 0.7184 (mtm) cc_final: 0.6783 (ttt) REVERT: F 699 ARG cc_start: 0.6392 (ttm110) cc_final: 0.5990 (ttm110) REVERT: G 36 TRP cc_start: 0.8566 (m100) cc_final: 0.8093 (m-10) REVERT: G 43 LYS cc_start: 0.7838 (mttt) cc_final: 0.7521 (mmmm) REVERT: G 100 MET cc_start: 0.8029 (mmt) cc_final: 0.7665 (mmt) REVERT: I 943 MET cc_start: 0.8289 (mmm) cc_final: 0.7986 (mmt) REVERT: I 1116 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8627 (t80) REVERT: J 270 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: J 627 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: J 696 MET cc_start: 0.7381 (mtt) cc_final: 0.6535 (ttt) REVERT: K 34 ILE cc_start: 0.9498 (mm) cc_final: 0.9111 (mm) REVERT: L 90 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7300 (tt0) outliers start: 119 outliers final: 97 residues processed: 404 average time/residue: 0.4027 time to fit residues: 259.3667 Evaluate side-chains 404 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 298 time to evaluate : 3.239 ------------------------------------------------------------------------------- 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 872 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1116 PHE 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 136 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR 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 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 86 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 792 GLN 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 1034 SER 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 125 ASN 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 140 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 269 ARG 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 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 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 GLN 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 852 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 1034 SER Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1151 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 I residue 1214 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 136 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 604 VAL 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 28 THR 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 20 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 Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN A1129 ASN D 76 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1169 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29544 Z= 0.353 Angle : 0.698 11.126 40140 Z= 0.355 Chirality : 0.047 0.417 4614 Planarity : 0.005 0.051 5133 Dihedral : 7.657 58.978 5262 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.58 % Favored : 94.11 % Rotamer: Outliers : 4.13 % Allowed : 11.41 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3582 helix: 2.26 (0.21), residues: 618 sheet: 0.63 (0.18), residues: 819 loop : -0.32 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 36 HIS 0.005 0.001 HIS A1146 PHE 0.018 0.002 PHE J 239 TYR 0.021 0.001 TYR I 909 ARG 0.007 0.001 ARG J 699 *********************** 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 435 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 308 time to evaluate : 3.627 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: 0.8626 (OUTLIER) cc_final: 0.8342 (ttmm) REVERT: A 932 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: A 1116 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8467 (t80) REVERT: C 43 LYS cc_start: 0.7617 (mttp) cc_final: 0.7271 (mmmm) REVERT: D 47 LEU cc_start: 0.7794 (mm) cc_final: 0.7325 (mt) REVERT: D 85 MET cc_start: 0.8420 (mmm) cc_final: 0.8154 (tpp) REVERT: D 89 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8102 (tm-30) REVERT: F 240 MET cc_start: 0.7822 (mmm) cc_final: 0.7570 (mmm) REVERT: F 269 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5771 (ptt90) REVERT: F 696 MET cc_start: 0.7177 (mtm) cc_final: 0.6747 (ttt) REVERT: F 699 ARG cc_start: 0.6475 (ttm110) cc_final: 0.6029 (ttm110) REVERT: G 36 TRP cc_start: 0.8598 (m100) cc_final: 0.8203 (m-10) REVERT: I 757 MET cc_start: 0.8154 (mmt) cc_final: 0.7487 (mmt) REVERT: I 913 MET cc_start: 0.7249 (mtp) cc_final: 0.7023 (mtp) REVERT: I 932 TYR cc_start: 0.6390 (m-10) cc_final: 0.6112 (m-80) REVERT: I 943 MET cc_start: 0.8345 (mmm) cc_final: 0.8033 (mmt) REVERT: I 1084 GLN cc_start: 0.8262 (tt0) cc_final: 0.7993 (tt0) REVERT: I 1116 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8744 (t80) REVERT: J 270 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: J 627 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: J 696 MET cc_start: 0.7331 (mtt) cc_final: 0.6793 (mtp) REVERT: K 34 ILE cc_start: 0.9326 (mm) cc_final: 0.8958 (mt) outliers start: 127 outliers final: 106 residues processed: 397 average time/residue: 0.4038 time to fit residues: 255.3876 Evaluate side-chains 408 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 295 time to evaluate : 3.317 ------------------------------------------------------------------------------- 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 872 THR Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1116 PHE 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 136 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 259 THR 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 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 THR 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 1034 SER 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 125 ASN 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 140 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 269 ARG 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 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 45 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 109 VAL 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 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 852 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 924 ILE Chi-restraints excluded: chain I residue 1034 SER Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1151 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 I residue 1214 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 136 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 604 VAL Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 303 optimal weight: 0.2980 chunk 319 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- 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 E1016 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29544 Z= 0.323 Angle : 0.686 12.034 40140 Z= 0.349 Chirality : 0.046 0.399 4614 Planarity : 0.005 0.051 5133 Dihedral : 7.472 59.438 5262 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.83 % Favored : 93.86 % Rotamer: Outliers : 3.84 % Allowed : 12.10 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3582 helix: 2.26 (0.21), residues: 618 sheet: 0.58 (0.18), residues: 825 loop : -0.44 (0.14), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.005 0.001 HIS A1146 PHE 0.027 0.002 PHE J 239 TYR 0.020 0.001 TYR I 777 ARG 0.007 0.001 ARG J 699 *********************** 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 426 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 308 time to evaluate : 3.149 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: 0.8603 (OUTLIER) cc_final: 0.8312 (ttmm) REVERT: A 932 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: A 1062 GLU cc_start: 0.7485 (mp0) cc_final: 0.7222 (mm-30) REVERT: A 1116 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8546 (t80) REVERT: A 1222 LEU cc_start: 0.7817 (tp) cc_final: 0.7595 (mt) REVERT: C 43 LYS cc_start: 0.7847 (mttp) cc_final: 0.7500 (mmmm) REVERT: D 85 MET cc_start: 0.8377 (mmm) cc_final: 0.8171 (tpp) REVERT: D 89 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8047 (tm-30) REVERT: F 269 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.5857 (ptt90) REVERT: F 696 MET cc_start: 0.7210 (mtm) cc_final: 0.7000 (mtp) REVERT: F 699 ARG cc_start: 0.6563 (ttm110) cc_final: 0.6347 (ttm110) REVERT: G 36 TRP cc_start: 0.8526 (m100) cc_final: 0.8325 (m100) REVERT: I 757 MET cc_start: 0.8125 (mmt) cc_final: 0.7483 (mmt) REVERT: I 932 TYR cc_start: 0.6445 (m-10) cc_final: 0.6128 (m-80) REVERT: I 943 MET cc_start: 0.8334 (mmm) cc_final: 0.8016 (mmt) REVERT: I 1116 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8649 (t80) REVERT: J 240 MET cc_start: 0.7940 (mmm) cc_final: 0.7340 (mmm) REVERT: J 270 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: J 627 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: J 696 MET cc_start: 0.7337 (mtt) cc_final: 0.6801 (mtp) REVERT: K 34 ILE cc_start: 0.9383 (mm) cc_final: 0.9110 (mm) REVERT: L 85 MET cc_start: 0.8851 (tpt) cc_final: 0.8606 (tpp) outliers start: 118 outliers final: 103 residues processed: 395 average time/residue: 0.4035 time to fit residues: 254.4162 Evaluate side-chains 402 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 292 time to evaluate : 2.951 ------------------------------------------------------------------------------- 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 862 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1116 PHE 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 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 259 THR 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 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 THR 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 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 125 ASN 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 140 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 269 ARG 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 717 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR 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 109 VAL 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 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 852 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 1034 SER Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1151 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 I residue 1214 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 136 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 604 VAL Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 355 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 283 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS E1016 ASN ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29544 Z= 0.202 Angle : 0.645 12.531 40140 Z= 0.327 Chirality : 0.045 0.416 4614 Planarity : 0.005 0.053 5133 Dihedral : 7.175 58.677 5262 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 3.06 % Allowed : 13.37 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3582 helix: 2.34 (0.21), residues: 636 sheet: 0.59 (0.18), residues: 813 loop : -0.41 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.004 0.001 HIS K 41 PHE 0.016 0.001 PHE J 239 TYR 0.021 0.001 TYR A 777 ARG 0.009 0.000 ARG J 699 ********************** 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 408 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 314 time to evaluate : 3.204 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: 0.8543 (OUTLIER) cc_final: 0.8236 (ttmm) REVERT: A 913 MET cc_start: 0.7429 (ttp) cc_final: 0.7140 (tmm) REVERT: A 932 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: A 1062 GLU cc_start: 0.7518 (mp0) cc_final: 0.7279 (mm-30) REVERT: A 1116 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8532 (t80) REVERT: A 1222 LEU cc_start: 0.7746 (tp) cc_final: 0.7542 (mt) REVERT: C 43 LYS cc_start: 0.7815 (mttp) cc_final: 0.7475 (mmmm) REVERT: D 89 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7938 (tm-30) REVERT: F 240 MET cc_start: 0.7833 (mmm) cc_final: 0.7541 (mmm) REVERT: F 269 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.5859 (ptt90) REVERT: F 696 MET cc_start: 0.7150 (mtm) cc_final: 0.6671 (ttt) REVERT: F 699 ARG cc_start: 0.6505 (ttm110) cc_final: 0.6062 (ttm110) REVERT: I 757 MET cc_start: 0.8120 (mmt) cc_final: 0.7488 (mmt) REVERT: I 932 TYR cc_start: 0.6288 (m-10) cc_final: 0.6027 (m-80) REVERT: I 943 MET cc_start: 0.8316 (mmm) cc_final: 0.7972 (mmt) REVERT: I 1084 GLN cc_start: 0.8211 (tt0) cc_final: 0.7963 (tt0) REVERT: I 1116 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8658 (t80) REVERT: J 240 MET cc_start: 0.7779 (mmm) cc_final: 0.7044 (mmm) REVERT: J 270 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: J 627 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: J 696 MET cc_start: 0.7306 (mtt) cc_final: 0.6786 (mtp) REVERT: K 34 ILE cc_start: 0.9347 (mm) cc_final: 0.9073 (mm) REVERT: K 43 LYS cc_start: 0.7469 (mmmt) cc_final: 0.6892 (pptt) REVERT: L 85 MET cc_start: 0.8843 (tpt) cc_final: 0.8452 (tpp) outliers start: 94 outliers final: 79 residues processed: 382 average time/residue: 0.4036 time to fit residues: 245.6181 Evaluate side-chains 389 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 303 time to evaluate : 3.515 ------------------------------------------------------------------------------- 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 862 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1116 PHE 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 736 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 97 THR 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 1034 SER 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 125 ASN Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 269 ARG 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 717 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 109 VAL 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 H residue 102 THR Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 1034 SER Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain I residue 1200 LEU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 136 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 717 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS 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 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 0.9990 chunk 301 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 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** ** 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 = 0.3811 r_free = 0.3811 target = 0.122822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092572 restraints weight = 63124.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092598 restraints weight = 36104.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093126 restraints weight = 33663.558| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29544 Z= 0.249 Angle : 0.659 12.455 40140 Z= 0.334 Chirality : 0.045 0.406 4614 Planarity : 0.005 0.061 5133 Dihedral : 7.142 59.982 5262 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.92 % Favored : 93.80 % Rotamer: Outliers : 3.25 % Allowed : 13.46 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3582 helix: 2.36 (0.21), residues: 636 sheet: 0.50 (0.18), residues: 828 loop : -0.46 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 36 HIS 0.004 0.001 HIS A1146 PHE 0.016 0.001 PHE J 239 TYR 0.025 0.001 TYR A 777 ARG 0.008 0.000 ARG J 699 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5691.49 seconds wall clock time: 104 minutes 39.82 seconds (6279.82 seconds total)