Starting phenix.real_space_refine on Wed Nov 20 00:28:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/11_2024/8g3p_29707.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/11_2024/8g3p_29707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/11_2024/8g3p_29707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/11_2024/8g3p_29707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/11_2024/8g3p_29707.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/11_2024/8g3p_29707.cif" } resolution = 2.5 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= 0.029 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12560 2.51 5 N 3448 2.21 5 O 4192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 40 Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "E" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "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: "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: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "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: "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: "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: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "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: "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: "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: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "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: "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: "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: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.71, per 1000 atoms: 0.67 Number of scatterers: 20321 At special positions: 0 Unit cell: (166.83, 166.83, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4192 8.00 N 3448 7.00 C 12560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.08 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.06 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=1.99 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.07 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.09 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.09 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.14 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.08 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.06 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=1.99 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.07 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.07 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.09 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.07 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.09 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.14 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.08 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=1.99 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.07 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.07 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.09 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.07 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.09 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.08 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.06 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.99 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.07 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.09 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.07 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.09 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.14 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA U 3 " - " MAN U 6 " " MAN U 6 " - " MAN U 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG M 1 " - " ASN A 86 " " NAG N 1 " - " ASN D 86 " " NAG O 1 " - " ASN E 86 " " NAG P 1 " - " ASN A 146 " " NAG Q 1 " - " ASN D 146 " " NAG R 1 " - " ASN E 146 " " NAG S 1 " - " ASN A 200 " " NAG T 1 " - " ASN D 200 " " NAG U 1 " - " ASN E 200 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN A 245 " " NAG Z 1 " - " ASN D 245 " " NAG a 1 " - " ASN E 245 " " NAG b 1 " - " ASN A 367 " " NAG c 1 " - " ASN D 367 " " NAG d 1 " - " ASN E 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 2.7 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.747A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.738A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.741A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.737A pdb=" N ASN E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.624A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.786A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 117 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.570A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.558A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.788A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP A 197 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.613A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP D 197 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.621A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.047A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 363 " --> pdb=" O TRP E 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.22 Time building geometry restraints manager: 6.93 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: 3493 1.32 - 1.44: 5751 1.44 - 1.57: 11360 1.57 - 1.69: 4 1.69 - 1.82: 144 Bond restraints: 20752 Sorted by residual: bond pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 1.460 1.508 -0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" N ILE E 176 " pdb=" CA ILE E 176 " ideal model delta sigma weight residual 1.460 1.507 -0.048 1.10e-02 8.26e+03 1.89e+01 bond pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C GLU B 162 " pdb=" O GLU B 162 " ideal model delta sigma weight residual 1.234 1.283 -0.049 1.24e-02 6.50e+03 1.59e+01 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21327 1.82 - 3.64: 5946 3.64 - 5.46: 766 5.46 - 7.28: 113 7.28 - 9.11: 16 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE D 397 " pdb=" CA ILE D 397 " pdb=" C ILE D 397 " ideal model delta sigma weight residual 111.67 106.32 5.35 9.50e-01 1.11e+00 3.17e+01 angle pdb=" N ILE A 397 " pdb=" CA ILE A 397 " pdb=" C ILE A 397 " ideal model delta sigma weight residual 111.67 106.35 5.32 9.50e-01 1.11e+00 3.14e+01 angle pdb=" CA ASP B 125 " pdb=" CB ASP B 125 " pdb=" CG ASP B 125 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.91e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.63: 12481 19.63 - 39.26: 539 39.26 - 58.90: 116 58.90 - 78.53: 52 78.53 - 98.16: 40 Dihedral angle restraints: 13228 sinusoidal: 6092 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASN E 441 " pdb=" C ASN E 441 " pdb=" N SER E 442 " pdb=" CA SER E 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN B 441 " pdb=" C ASN B 441 " pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN D 441 " pdb=" C ASN D 441 " pdb=" N SER D 442 " pdb=" CA SER D 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 13225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2162 0.091 - 0.182: 1018 0.182 - 0.273: 92 0.273 - 0.364: 8 0.364 - 0.454: 12 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.79e+01 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 MAN s 4 " pdb=" O3 BMA s 3 " pdb=" C2 MAN s 4 " pdb=" O5 MAN s 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.64e+01 ... (remaining 3289 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 281 " -0.084 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR D 281 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 281 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR D 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR D 281 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 281 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 281 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 281 " 0.085 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR B 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 281 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.085 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR E 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.057 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4924 2.83 - 3.35: 19156 3.35 - 3.87: 36030 3.87 - 4.38: 44702 4.38 - 4.90: 72604 Nonbonded interactions: 177416 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP B 293 " pdb="CA CA B2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D2000 " model vdw 2.316 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.316 2.510 nonbonded pdb=" O HIS D 347 " pdb="CA CA D2000 " model vdw 2.317 2.510 ... (remaining 177411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 82 through 469 or resid 501)) selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' 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 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.810 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: 0.440 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 50.170 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.180 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.061 20752 Z= 0.947 Angle : 1.637 9.105 28168 Z= 1.062 Chirality : 0.094 0.454 3292 Planarity : 0.010 0.071 3528 Dihedral : 13.928 98.160 8552 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.86 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.75 (0.16), residues: 2488 helix: -0.11 (0.97), residues: 24 sheet: -0.04 (0.16), residues: 1008 loop : -0.81 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.012 TRP J 97 HIS 0.021 0.006 HIS A 168 PHE 0.060 0.013 PHE E 205 TYR 0.085 0.013 TYR B 281 ARG 0.019 0.003 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.9335 (ttmt) cc_final: 0.9135 (mtpm) REVERT: I 70 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 400 ARG cc_start: 0.9264 (ptm-80) cc_final: 0.9027 (ptm160) REVERT: F 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: J 70 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9029 (ptm160) REVERT: G 23 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9133 (mtpm) REVERT: K 70 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9028 (ptm160) REVERT: H 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: L 70 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7811 (mt-10) REVERT: E 400 ARG cc_start: 0.9265 (ptm-80) cc_final: 0.9026 (ptm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 1.5498 time to fit residues: 499.9916 Evaluate side-chains 213 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 65 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS F 32 GLN F 65 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS G 32 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS H 32 GLN H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 20752 Z= 0.238 Angle : 0.673 8.224 28168 Z= 0.360 Chirality : 0.047 0.262 3292 Planarity : 0.004 0.045 3528 Dihedral : 8.876 73.503 4260 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 1.69 % Allowed : 6.88 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.33 (0.16), residues: 2488 helix: 0.27 (0.88), residues: 24 sheet: -0.05 (0.15), residues: 1068 loop : -0.27 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 178 HIS 0.003 0.001 HIS A 168 PHE 0.014 0.002 PHE D 410 TYR 0.013 0.002 TYR C 95 ARG 0.008 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 17 GLU cc_start: 0.8141 (mp0) cc_final: 0.7863 (mp0) REVERT: I 24 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7984 (ttm110) REVERT: I 81 GLU cc_start: 0.9239 (pm20) cc_final: 0.8942 (pp20) REVERT: J 17 GLU cc_start: 0.8135 (mp0) cc_final: 0.7856 (mp0) REVERT: J 24 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7980 (ttm110) REVERT: J 81 GLU cc_start: 0.9240 (pm20) cc_final: 0.8941 (pp20) REVERT: K 17 GLU cc_start: 0.8136 (mp0) cc_final: 0.7860 (mp0) REVERT: K 24 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7981 (ttm110) REVERT: K 81 GLU cc_start: 0.9241 (pm20) cc_final: 0.8924 (pp20) REVERT: L 17 GLU cc_start: 0.8138 (mp0) cc_final: 0.7859 (mp0) REVERT: L 24 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7950 (ttm110) REVERT: L 81 GLU cc_start: 0.9241 (pm20) cc_final: 0.8949 (pp20) outliers start: 36 outliers final: 12 residues processed: 245 average time/residue: 1.7100 time to fit residues: 465.4396 Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.0370 chunk 69 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 468 HIS F 65 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 468 HIS H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 HIS E 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20752 Z= 0.314 Angle : 0.646 5.139 28168 Z= 0.346 Chirality : 0.047 0.251 3292 Planarity : 0.004 0.031 3528 Dihedral : 8.178 65.880 4260 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 2.11 % Allowed : 8.71 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.42 (0.16), residues: 2488 helix: 0.20 (0.82), residues: 24 sheet: -0.13 (0.15), residues: 1068 loop : -0.31 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 178 HIS 0.004 0.001 HIS B 168 PHE 0.015 0.002 PHE D 410 TYR 0.017 0.002 TYR A 121 ARG 0.008 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.9177 (mtpm) cc_final: 0.8961 (mtpm) REVERT: C 65 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8473 (tp-100) REVERT: I 17 GLU cc_start: 0.8227 (mp0) cc_final: 0.7919 (mp0) REVERT: I 24 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8297 (ttm110) REVERT: I 79 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8026 (mp-120) REVERT: I 81 GLU cc_start: 0.9238 (pm20) cc_final: 0.8948 (pp20) REVERT: I 107 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7109 (mm) REVERT: F 23 LYS cc_start: 0.9178 (mtpm) cc_final: 0.8962 (mtpm) REVERT: J 17 GLU cc_start: 0.8224 (mp0) cc_final: 0.7916 (mp0) REVERT: J 24 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8285 (ttm110) REVERT: J 79 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8027 (mp-120) REVERT: J 81 GLU cc_start: 0.9239 (pm20) cc_final: 0.8944 (pp20) REVERT: J 107 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7062 (mm) REVERT: G 23 LYS cc_start: 0.9178 (mtpm) cc_final: 0.8963 (mtpm) REVERT: G 46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8621 (tt0) REVERT: G 65 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8466 (tp-100) REVERT: K 17 GLU cc_start: 0.8226 (mp0) cc_final: 0.7918 (mp0) REVERT: K 24 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8282 (ttm110) REVERT: K 79 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8029 (mp-120) REVERT: K 81 GLU cc_start: 0.9239 (pm20) cc_final: 0.8947 (pp20) REVERT: K 107 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7060 (mm) REVERT: H 90 ASP cc_start: 0.8115 (m-30) cc_final: 0.7815 (m-30) REVERT: L 17 GLU cc_start: 0.8223 (mp0) cc_final: 0.7915 (mp0) REVERT: L 24 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8300 (ttm110) REVERT: L 79 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8054 (mp-120) REVERT: L 81 GLU cc_start: 0.9239 (pm20) cc_final: 0.8946 (pp20) REVERT: L 107 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7063 (mm) outliers start: 45 outliers final: 20 residues processed: 229 average time/residue: 1.7313 time to fit residues: 439.2455 Evaluate side-chains 226 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 274 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20752 Z= 0.222 Angle : 0.598 5.917 28168 Z= 0.317 Chirality : 0.045 0.257 3292 Planarity : 0.004 0.037 3528 Dihedral : 7.605 58.512 4260 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.17 % Allowed : 10.07 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.37 (0.16), residues: 2488 helix: -0.04 (0.77), residues: 24 sheet: -0.21 (0.15), residues: 1088 loop : -0.16 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 178 HIS 0.003 0.001 HIS A 468 PHE 0.014 0.002 PHE E 410 TYR 0.012 0.001 TYR D 121 ARG 0.009 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 17 GLU cc_start: 0.8272 (mp0) cc_final: 0.7954 (mp0) REVERT: I 79 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8059 (mp-120) REVERT: I 81 GLU cc_start: 0.9230 (pm20) cc_final: 0.8940 (pp20) REVERT: I 107 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7126 (mm) REVERT: J 17 GLU cc_start: 0.8270 (mp0) cc_final: 0.7951 (mp0) REVERT: J 79 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8058 (mp-120) REVERT: J 81 GLU cc_start: 0.9230 (pm20) cc_final: 0.8940 (pp20) REVERT: J 107 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7125 (mm) REVERT: G 46 GLU cc_start: 0.8909 (tt0) cc_final: 0.8674 (tt0) REVERT: K 17 GLU cc_start: 0.8259 (mp0) cc_final: 0.7939 (mp0) REVERT: K 79 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8056 (mp-120) REVERT: K 81 GLU cc_start: 0.9230 (pm20) cc_final: 0.8940 (pp20) REVERT: K 107 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7126 (mm) REVERT: L 17 GLU cc_start: 0.8272 (mp0) cc_final: 0.7953 (mp0) REVERT: L 79 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8069 (mp-120) REVERT: L 81 GLU cc_start: 0.9231 (pm20) cc_final: 0.8940 (pp20) REVERT: L 107 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7129 (mm) outliers start: 25 outliers final: 17 residues processed: 220 average time/residue: 1.6985 time to fit residues: 415.8042 Evaluate side-chains 217 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN B 468 HIS F 32 GLN A 468 HIS G 32 GLN D 468 HIS H 32 GLN E 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20752 Z= 0.338 Angle : 0.637 6.095 28168 Z= 0.337 Chirality : 0.047 0.243 3292 Planarity : 0.004 0.044 3528 Dihedral : 7.718 59.251 4260 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 1.36 % Allowed : 11.38 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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 (0.16), residues: 2488 helix: 0.04 (0.77), residues: 24 sheet: -0.28 (0.15), residues: 1088 loop : -0.14 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS D 468 PHE 0.015 0.002 PHE E 410 TYR 0.015 0.002 TYR D 121 ARG 0.010 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 17 GLU cc_start: 0.8293 (mp0) cc_final: 0.7931 (mp0) REVERT: I 79 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8038 (mp-120) REVERT: I 81 GLU cc_start: 0.9236 (pm20) cc_final: 0.8934 (pp20) REVERT: I 107 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7077 (mm) REVERT: J 17 GLU cc_start: 0.8292 (mp0) cc_final: 0.7936 (mp0) REVERT: J 79 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8035 (mp-120) REVERT: J 81 GLU cc_start: 0.9238 (pm20) cc_final: 0.8936 (pp20) REVERT: J 107 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7074 (mm) REVERT: G 46 GLU cc_start: 0.8938 (tt0) cc_final: 0.8715 (tt0) REVERT: K 17 GLU cc_start: 0.8288 (mp0) cc_final: 0.7929 (mp0) REVERT: K 79 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8034 (mp-120) REVERT: K 81 GLU cc_start: 0.9237 (pm20) cc_final: 0.8935 (pp20) REVERT: K 107 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7074 (mm) REVERT: L 17 GLU cc_start: 0.8288 (mp0) cc_final: 0.7927 (mp0) REVERT: L 79 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8034 (mp-120) REVERT: L 81 GLU cc_start: 0.9237 (pm20) cc_final: 0.8935 (pp20) REVERT: L 107 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7078 (mm) outliers start: 29 outliers final: 20 residues processed: 213 average time/residue: 1.5957 time to fit residues: 379.5512 Evaluate side-chains 217 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 441 ASN E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20752 Z= 0.359 Angle : 0.642 6.280 28168 Z= 0.338 Chirality : 0.047 0.227 3292 Planarity : 0.004 0.047 3528 Dihedral : 7.766 59.784 4260 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.26 % Allowed : 11.38 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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 (0.16), residues: 2488 helix: 0.16 (0.79), residues: 24 sheet: -0.30 (0.15), residues: 1080 loop : -0.12 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 178 HIS 0.002 0.001 HIS D 468 PHE 0.016 0.002 PHE B 410 TYR 0.015 0.002 TYR A 121 ARG 0.011 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 MET cc_start: 0.8534 (mmm) cc_final: 0.8314 (mmm) REVERT: I 17 GLU cc_start: 0.8320 (mp0) cc_final: 0.8059 (mp0) REVERT: I 24 ARG cc_start: 0.8582 (ttm110) cc_final: 0.8357 (ttm110) REVERT: I 61 ARG cc_start: 0.8792 (ptm-80) cc_final: 0.8476 (ptm-80) REVERT: I 79 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8188 (mm-40) REVERT: I 81 GLU cc_start: 0.9234 (pm20) cc_final: 0.8927 (pp20) REVERT: I 107 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7238 (pp) REVERT: J 17 GLU cc_start: 0.8315 (mp0) cc_final: 0.8054 (mp0) REVERT: J 61 ARG cc_start: 0.8791 (ptm-80) cc_final: 0.8449 (ptm-80) REVERT: J 79 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8179 (mm-40) REVERT: J 81 GLU cc_start: 0.9235 (pm20) cc_final: 0.8936 (pp20) REVERT: J 107 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7246 (pp) REVERT: G 46 GLU cc_start: 0.8947 (tt0) cc_final: 0.8719 (tt0) REVERT: K 4 MET cc_start: 0.8523 (mmm) cc_final: 0.8303 (mmm) REVERT: K 17 GLU cc_start: 0.8318 (mp0) cc_final: 0.8055 (mp0) REVERT: K 61 ARG cc_start: 0.8796 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: K 79 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8178 (mm-40) REVERT: K 81 GLU cc_start: 0.9234 (pm20) cc_final: 0.8936 (pp20) REVERT: K 107 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7250 (pp) REVERT: L 17 GLU cc_start: 0.8313 (mp0) cc_final: 0.8052 (mp0) REVERT: L 79 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8185 (mm-40) REVERT: L 81 GLU cc_start: 0.9231 (pm20) cc_final: 0.8935 (pp20) REVERT: L 107 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7248 (pp) outliers start: 27 outliers final: 22 residues processed: 219 average time/residue: 1.5773 time to fit residues: 389.0348 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN B 441 ASN B 468 HIS A 441 ASN A 468 HIS G 65 GLN D 441 ASN D 468 HIS E 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20752 Z= 0.298 Angle : 0.634 6.695 28168 Z= 0.333 Chirality : 0.046 0.232 3292 Planarity : 0.004 0.048 3528 Dihedral : 7.529 58.106 4260 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 1.50 % Allowed : 12.08 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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 (0.16), residues: 2488 helix: 0.13 (0.78), residues: 24 sheet: -0.31 (0.15), residues: 1080 loop : -0.11 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.003 0.001 HIS E 468 PHE 0.015 0.002 PHE B 410 TYR 0.013 0.002 TYR D 121 ARG 0.013 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 17 GLU cc_start: 0.8344 (mp0) cc_final: 0.8068 (mp0) REVERT: I 61 ARG cc_start: 0.8803 (ptm-80) cc_final: 0.8446 (ptm-80) REVERT: I 79 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8220 (mm-40) REVERT: I 81 GLU cc_start: 0.9230 (pm20) cc_final: 0.8936 (pp20) REVERT: I 107 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7302 (pp) REVERT: F 13 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9091 (mp0) REVERT: J 17 GLU cc_start: 0.8333 (mp0) cc_final: 0.8058 (mp0) REVERT: J 61 ARG cc_start: 0.8796 (ptm-80) cc_final: 0.8431 (ptm-80) REVERT: J 79 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8215 (mm-40) REVERT: J 81 GLU cc_start: 0.9231 (pm20) cc_final: 0.8938 (pp20) REVERT: J 107 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7308 (pp) REVERT: G 46 GLU cc_start: 0.8935 (tt0) cc_final: 0.8710 (tt0) REVERT: K 17 GLU cc_start: 0.8336 (mp0) cc_final: 0.8059 (mp0) REVERT: K 61 ARG cc_start: 0.8796 (ptm-80) cc_final: 0.8485 (ptm-80) REVERT: K 79 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8217 (mm-40) REVERT: K 81 GLU cc_start: 0.9231 (pm20) cc_final: 0.8938 (pp20) REVERT: K 107 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7311 (pp) REVERT: L 17 GLU cc_start: 0.8336 (mp0) cc_final: 0.8057 (mp0) REVERT: L 79 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8007 (mp-120) REVERT: L 81 GLU cc_start: 0.9231 (pm20) cc_final: 0.8924 (pp20) REVERT: L 107 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7312 (pp) outliers start: 32 outliers final: 24 residues processed: 219 average time/residue: 1.5920 time to fit residues: 389.6157 Evaluate side-chains 224 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20752 Z= 0.208 Angle : 0.605 7.184 28168 Z= 0.315 Chirality : 0.045 0.234 3292 Planarity : 0.004 0.051 3528 Dihedral : 6.952 57.596 4260 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 1.31 % Allowed : 12.64 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.35 (0.16), residues: 2488 helix: -0.68 (0.76), residues: 28 sheet: -0.24 (0.15), residues: 1080 loop : -0.08 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.003 0.001 HIS B 468 PHE 0.023 0.002 PHE H 64 TYR 0.011 0.001 TYR B 121 ARG 0.013 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9075 (mp0) REVERT: C 73 ASP cc_start: 0.5717 (t0) cc_final: 0.5242 (t0) REVERT: I 17 GLU cc_start: 0.8372 (mp0) cc_final: 0.8096 (mp0) REVERT: I 61 ARG cc_start: 0.8820 (ptm-80) cc_final: 0.8443 (ptm-80) REVERT: I 79 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8233 (mm-40) REVERT: I 81 GLU cc_start: 0.9239 (pm20) cc_final: 0.8953 (pp20) REVERT: I 107 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7441 (pp) REVERT: F 13 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9085 (mp0) REVERT: F 73 ASP cc_start: 0.5736 (t0) cc_final: 0.5258 (t0) REVERT: J 17 GLU cc_start: 0.8368 (mp0) cc_final: 0.8094 (mp0) REVERT: J 61 ARG cc_start: 0.8824 (ptm-80) cc_final: 0.8444 (ptm-80) REVERT: J 79 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8232 (mm-40) REVERT: J 81 GLU cc_start: 0.9240 (pm20) cc_final: 0.8945 (pp20) REVERT: J 107 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7443 (pp) REVERT: G 13 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9089 (mp0) REVERT: G 46 GLU cc_start: 0.8917 (tt0) cc_final: 0.8648 (tt0) REVERT: G 73 ASP cc_start: 0.5714 (t0) cc_final: 0.5240 (t0) REVERT: K 17 GLU cc_start: 0.8368 (mp0) cc_final: 0.8094 (mp0) REVERT: K 61 ARG cc_start: 0.8836 (ptm-80) cc_final: 0.8446 (ptm-80) REVERT: K 79 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8210 (mm-40) REVERT: K 81 GLU cc_start: 0.9245 (pm20) cc_final: 0.8950 (pp20) REVERT: K 107 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7444 (pp) REVERT: H 73 ASP cc_start: 0.5698 (t0) cc_final: 0.5226 (t0) REVERT: L 17 GLU cc_start: 0.8363 (mp0) cc_final: 0.8086 (mp0) REVERT: L 79 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7953 (mp-120) REVERT: L 81 GLU cc_start: 0.9242 (pm20) cc_final: 0.8940 (pp20) REVERT: L 107 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7439 (pp) outliers start: 28 outliers final: 22 residues processed: 227 average time/residue: 1.5656 time to fit residues: 398.4627 Evaluate side-chains 228 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20752 Z= 0.253 Angle : 0.626 7.469 28168 Z= 0.326 Chirality : 0.045 0.233 3292 Planarity : 0.004 0.061 3528 Dihedral : 6.933 57.125 4260 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.31 % Allowed : 13.06 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.31 (0.16), residues: 2488 helix: -0.70 (0.77), residues: 28 sheet: -0.20 (0.15), residues: 1080 loop : -0.07 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 178 HIS 0.004 0.001 HIS B 468 PHE 0.021 0.002 PHE H 64 TYR 0.012 0.001 TYR D 121 ARG 0.012 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9075 (mp0) REVERT: C 73 ASP cc_start: 0.5652 (t0) cc_final: 0.5214 (t0) REVERT: I 4 MET cc_start: 0.8624 (mmm) cc_final: 0.8381 (mmm) REVERT: I 17 GLU cc_start: 0.8386 (mp0) cc_final: 0.8096 (mp0) REVERT: I 61 ARG cc_start: 0.8847 (ptm-80) cc_final: 0.8413 (ptm-80) REVERT: I 79 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8190 (mm-40) REVERT: I 81 GLU cc_start: 0.9219 (pm20) cc_final: 0.8913 (pp20) REVERT: I 107 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7444 (pp) REVERT: F 13 GLU cc_start: 0.9354 (mt-10) cc_final: 0.9081 (mp0) REVERT: F 73 ASP cc_start: 0.5690 (t0) cc_final: 0.5214 (t0) REVERT: J 17 GLU cc_start: 0.8372 (mp0) cc_final: 0.8090 (mp0) REVERT: J 61 ARG cc_start: 0.8846 (ptm-80) cc_final: 0.8463 (ptm-80) REVERT: J 79 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8206 (mm-40) REVERT: J 81 GLU cc_start: 0.9223 (pm20) cc_final: 0.8916 (pp20) REVERT: J 107 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7444 (pp) REVERT: G 13 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9080 (mp0) REVERT: G 46 GLU cc_start: 0.8924 (tt0) cc_final: 0.8703 (tt0) REVERT: G 73 ASP cc_start: 0.5664 (t0) cc_final: 0.5227 (t0) REVERT: K 17 GLU cc_start: 0.8384 (mp0) cc_final: 0.8103 (mp0) REVERT: K 61 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8482 (ptm-80) REVERT: K 79 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8202 (mm-40) REVERT: K 81 GLU cc_start: 0.9224 (pm20) cc_final: 0.8916 (pp20) REVERT: K 107 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7444 (pp) REVERT: H 73 ASP cc_start: 0.5627 (t0) cc_final: 0.5153 (t0) REVERT: L 17 GLU cc_start: 0.8372 (mp0) cc_final: 0.8090 (mp0) REVERT: L 79 GLN cc_start: 0.8591 (mm-40) cc_final: 0.7975 (mp-120) REVERT: L 81 GLU cc_start: 0.9235 (pm20) cc_final: 0.8925 (pp20) REVERT: L 107 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7446 (pp) outliers start: 28 outliers final: 22 residues processed: 221 average time/residue: 1.6518 time to fit residues: 409.2134 Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20752 Z= 0.203 Angle : 0.613 7.602 28168 Z= 0.318 Chirality : 0.045 0.236 3292 Planarity : 0.004 0.063 3528 Dihedral : 6.764 56.935 4260 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 1.26 % Allowed : 13.16 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.27 (0.17), residues: 2488 helix: -0.71 (0.76), residues: 28 sheet: -0.17 (0.15), residues: 1080 loop : -0.04 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.004 0.001 HIS E 468 PHE 0.021 0.002 PHE H 64 TYR 0.011 0.001 TYR D 121 ARG 0.016 0.001 ARG K 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9078 (mp0) REVERT: C 73 ASP cc_start: 0.5667 (t0) cc_final: 0.5216 (t0) REVERT: I 17 GLU cc_start: 0.8389 (mp0) cc_final: 0.8110 (mp0) REVERT: I 61 ARG cc_start: 0.8869 (ptm-80) cc_final: 0.8501 (ptm-80) REVERT: I 79 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8223 (mm-40) REVERT: I 81 GLU cc_start: 0.9215 (pm20) cc_final: 0.8915 (pp20) REVERT: I 107 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7493 (pp) REVERT: F 13 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9079 (mp0) REVERT: F 73 ASP cc_start: 0.5656 (t0) cc_final: 0.5195 (t0) REVERT: J 17 GLU cc_start: 0.8389 (mp0) cc_final: 0.8105 (mp0) REVERT: J 61 ARG cc_start: 0.8874 (ptm-80) cc_final: 0.8506 (ptm-80) REVERT: J 79 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8199 (mm-40) REVERT: J 81 GLU cc_start: 0.9219 (pm20) cc_final: 0.8917 (pp20) REVERT: J 107 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7490 (pp) REVERT: G 13 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9078 (mp0) REVERT: G 46 GLU cc_start: 0.8917 (tt0) cc_final: 0.8660 (tt0) REVERT: G 73 ASP cc_start: 0.5665 (t0) cc_final: 0.5213 (t0) REVERT: K 17 GLU cc_start: 0.8388 (mp0) cc_final: 0.8101 (mp0) REVERT: K 61 ARG cc_start: 0.8883 (ptm-80) cc_final: 0.8507 (ptm-80) REVERT: K 79 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8209 (mm-40) REVERT: K 81 GLU cc_start: 0.9221 (pm20) cc_final: 0.8917 (pp20) REVERT: K 107 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7492 (pp) REVERT: H 13 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9076 (mp0) REVERT: H 73 ASP cc_start: 0.5591 (t0) cc_final: 0.5132 (t0) REVERT: L 17 GLU cc_start: 0.8375 (mp0) cc_final: 0.8091 (mp0) REVERT: L 79 GLN cc_start: 0.8588 (mm-40) cc_final: 0.7930 (mp-120) REVERT: L 81 GLU cc_start: 0.9219 (pm20) cc_final: 0.8906 (pp20) REVERT: L 107 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7492 (pp) outliers start: 27 outliers final: 21 residues processed: 222 average time/residue: 1.6186 time to fit residues: 400.8274 Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.052623 restraints weight = 38026.197| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.64 r_work: 0.2572 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20752 Z= 0.438 Angle : 0.695 8.219 28168 Z= 0.363 Chirality : 0.048 0.232 3292 Planarity : 0.004 0.066 3528 Dihedral : 7.500 56.923 4260 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.34 % Rotamer: Outliers : 1.26 % Allowed : 13.34 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.42 (0.16), residues: 2488 helix: 0.12 (0.78), residues: 24 sheet: -0.27 (0.15), residues: 1080 loop : -0.18 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 178 HIS 0.004 0.001 HIS E 468 PHE 0.020 0.002 PHE H 64 TYR 0.015 0.002 TYR B 121 ARG 0.012 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7483.81 seconds wall clock time: 136 minutes 40.18 seconds (8200.18 seconds total)