Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 16:58:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dto_27706/08_2023/8dto_27706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dto_27706/08_2023/8dto_27706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dto_27706/08_2023/8dto_27706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dto_27706/08_2023/8dto_27706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dto_27706/08_2023/8dto_27706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dto_27706/08_2023/8dto_27706.pdb" } resolution = 3.57 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= 0.001 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12990 2.51 5 N 3366 2.21 5 O 4435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 20923 Number of models: 1 Model: "" Number of chains: 54 Chain: "E" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" 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 chiralities: 2 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "w" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.47, per 1000 atoms: 0.50 Number of scatterers: 20923 At special positions: 0 Unit cell: (163.08, 157.68, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4435 8.00 N 3366 7.00 C 12990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 444 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA p 3 " - " MAN p 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 5 " " BMA S 3 " - " MAN S 7 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 5 " " BMA f 3 " - " MAN f 7 " " BMA h 3 " - " MAN h 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 5 " " BMA t 3 " - " MAN t 7 " " BMA v 3 " - " MAN v 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 V 2 " - " NAG V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " NAG i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " NAG w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 701 " - " ASN A 355 " " NAG A 702 " - " ASN A 234 " " NAG A 703 " - " ASN A 396 " " NAG E 701 " - " ASN E 355 " " NAG E 702 " - " ASN E 234 " " NAG E 703 " - " ASN E 339 " " NAG E 704 " - " ASN E 396 " " NAG I 701 " - " ASN I 355 " " NAG I 702 " - " ASN I 234 " " NAG I 703 " - " ASN I 276 " " NAG I 704 " - " ASN I 339 " " NAG I 705 " - " ASN I 396 " " NAG M 1 " - " ASN E 441 " " NAG N 1 " - " ASN E 301 " " NAG O 1 " - " ASN E 154 " " NAG P 1 " - " ASN E 197 " " NAG Q 1 " - " ASN E 392 " " NAG R 1 " - " ASN E 241 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 158 " " NAG V 1 " - " ASN E 447 " " NAG W 1 " - " ASN E 276 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN E 362 " " NAG Z 1 " - " ASN A 441 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 154 " " NAG c 1 " - " ASN A 197 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 241 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 158 " " NAG h 1 " - " ASN A 262 " " NAG i 1 " - " ASN A 447 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 362 " " NAG l 1 " - " ASN A 276 " " NAG m 1 " - " ASN A 339 " " NAG n 1 " - " ASN I 441 " " NAG o 1 " - " ASN I 301 " " NAG p 1 " - " ASN I 154 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 392 " " NAG s 1 " - " ASN I 241 " " NAG t 1 " - " ASN I 332 " " NAG u 1 " - " ASN I 158 " " NAG v 1 " - " ASN I 262 " " NAG w 1 " - " ASN I 447 " " NAG x 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 362 " Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 2.9 seconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 45 sheets defined 17.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.554A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.035A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 Processing helix chain 'E' and resid 474 through 480 removed outlier: 4.064A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.666A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.626A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.932A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.872A pdb=" N ALA H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.023A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLY A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.941A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.684A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.635A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.733A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.854A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.609A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 335 through 351 removed outlier: 4.108A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.681A pdb=" N SER I 480 " --> pdb=" O ASP I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.969A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.656A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.982A pdb=" N SER J 636 " --> pdb=" O ASP J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.611A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.862A pdb=" N ALA L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.337A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.984A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.597A pdb=" N LEU E 260 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR E 443 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N ILE E 294 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG E 445 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL E 292 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN E 447 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N THR E 290 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 449 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 420 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE E 382 " --> pdb=" O LYS E 420 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.818A pdb=" N THR E 449 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N THR E 290 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN E 447 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL E 292 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG E 445 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N ILE E 294 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR E 443 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 466 " --> pdb=" O ASP E 456 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR E 357 " --> pdb=" O GLU E 465 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE E 467 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS E 360 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR G 116 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.553A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.497A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.596A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AC3, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.816A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.041A pdb=" N GLY A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.041A pdb=" N GLY A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.623A pdb=" N PHE A 382 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 420 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 301 through 302 removed outlier: 4.057A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AC9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.779A pdb=" N LYS C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.775A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AD5, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 75 through 76 removed outlier: 7.427A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE1, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.954A pdb=" N THR I 202 " --> pdb=" O TYR I 434 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.006A pdb=" N GLY I 450 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N THR I 443 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE I 294 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG I 445 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL I 292 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ASN I 447 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR I 290 " --> pdb=" O ASN I 447 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR I 449 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.811A pdb=" N THR I 449 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR I 290 " --> pdb=" O ASN I 447 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ASN I 447 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL I 292 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG I 445 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE I 294 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N THR I 443 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 305 through 309 removed outlier: 3.759A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.693A pdb=" N LYS K 12 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 698 hydrogen bonds defined for protein. 1851 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: 7.55 Time building geometry restraints manager: 11.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6356 1.34 - 1.46: 5312 1.46 - 1.58: 9495 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 21340 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.331 1.367 -0.036 7.90e-03 1.60e+04 2.04e+01 bond pdb=" C1 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C1 NAG w 3 " pdb=" O5 NAG w 3 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG I 703 " pdb=" O5 NAG I 703 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG i 3 " pdb=" O5 NAG i 3 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.71e+00 ... (remaining 21335 not shown) Histogram of bond angle deviations from ideal: 94.88 - 102.77: 81 102.77 - 110.66: 7574 110.66 - 118.55: 10143 118.55 - 126.44: 10807 126.44 - 134.33: 420 Bond angle restraints: 29025 Sorted by residual: angle pdb=" C THR I 257 " pdb=" N GLN I 258 " pdb=" CA GLN I 258 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C ASN I 276 " pdb=" N LEU I 277 " pdb=" CA LEU I 277 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N SER A 388 " pdb=" CA SER A 388 " pdb=" C SER A 388 " ideal model delta sigma weight residual 114.04 109.27 4.77 1.24e+00 6.50e-01 1.48e+01 angle pdb=" CA LEU I 259 " pdb=" CB LEU I 259 " pdb=" CG LEU I 259 " ideal model delta sigma weight residual 116.30 129.48 -13.18 3.50e+00 8.16e-02 1.42e+01 angle pdb=" CB MET I 474 " pdb=" CG MET I 474 " pdb=" SD MET I 474 " ideal model delta sigma weight residual 112.70 123.80 -11.10 3.00e+00 1.11e-01 1.37e+01 ... (remaining 29020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 10310 16.41 - 32.83: 1033 32.83 - 49.24: 257 49.24 - 65.65: 38 65.65 - 82.07: 17 Dihedral angle restraints: 11655 sinusoidal: 4602 harmonic: 7053 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.84 -59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.29 -58.29 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 444 " pdb=" CB CYS I 444 " ideal model delta sinusoidal sigma weight residual -86.00 -36.15 -49.85 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 11652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3016 0.075 - 0.149: 581 0.149 - 0.224: 58 0.224 - 0.299: 30 0.299 - 0.374: 5 Chirality restraints: 3690 Sorted by residual: chirality pdb=" C1 NAG I 704 " pdb=" ND2 ASN I 339 " pdb=" C2 NAG I 704 " pdb=" O5 NAG I 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN A 339 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3687 not shown) Planarity restraints: 3542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO E 43 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 176 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO E 177 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 177 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 177 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO L 46 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.025 5.00e-02 4.00e+02 ... (remaining 3539 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3919 2.77 - 3.30: 18111 3.30 - 3.84: 34342 3.84 - 4.37: 38167 4.37 - 4.90: 67764 Nonbonded interactions: 162303 Sorted by model distance: nonbonded pdb=" O MET I 369 " pdb=" OG1 THR I 373 " model vdw 2.241 2.440 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.245 2.440 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.248 2.440 nonbonded pdb=" O VAL I 36 " pdb=" OG1 THR J 606 " model vdw 2.253 2.440 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.258 2.440 ... (remaining 162298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 33 through 504 or resid 701 through 703)) selection = (chain 'I' and (resid 33 through 504 or resid 701 through 703)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Z' selection = chain 'n' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'u' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'b' selection = chain 'h' selection = chain 'p' selection = chain 'v' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'y' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.890 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 56.450 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.007 0.053 21340 Z= 0.411 Angle : 0.941 13.178 29025 Z= 0.437 Chirality : 0.063 0.374 3690 Planarity : 0.005 0.050 3492 Dihedral : 13.865 82.067 7020 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2415 helix: -0.46 (0.24), residues: 375 sheet: -0.41 (0.20), residues: 678 loop : -1.38 (0.16), residues: 1362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.275 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3039 time to fit residues: 42.5666 Evaluate side-chains 66 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS E 262 ASN A 258 GLN C 3 GLN I 229 ASN I 424 ASN J 540 GLN K 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 21340 Z= 0.402 Angle : 0.642 7.807 29025 Z= 0.321 Chirality : 0.045 0.252 3690 Planarity : 0.004 0.048 3492 Dihedral : 4.879 20.271 2637 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2415 helix: 0.58 (0.28), residues: 375 sheet: -0.37 (0.19), residues: 693 loop : -1.30 (0.17), residues: 1347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 2.437 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 0.2847 time to fit residues: 35.1589 Evaluate side-chains 67 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 2.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2189 time to fit residues: 4.2747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 21340 Z= 0.255 Angle : 0.552 6.862 29025 Z= 0.276 Chirality : 0.043 0.236 3690 Planarity : 0.003 0.038 3492 Dihedral : 4.609 19.491 2637 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.86 (0.17), residues: 2415 helix: 1.11 (0.29), residues: 375 sheet: -0.39 (0.19), residues: 711 loop : -1.17 (0.17), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 2.428 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.2886 time to fit residues: 35.7468 Evaluate side-chains 66 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2179 time to fit residues: 4.3690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 21340 Z= 0.274 Angle : 0.558 6.305 29025 Z= 0.277 Chirality : 0.043 0.226 3690 Planarity : 0.003 0.036 3492 Dihedral : 4.538 19.239 2637 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.76 (0.17), residues: 2415 helix: 1.31 (0.29), residues: 375 sheet: -0.39 (0.19), residues: 717 loop : -1.11 (0.17), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 2.455 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 71 average time/residue: 0.2963 time to fit residues: 37.8183 Evaluate side-chains 65 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2247 time to fit residues: 4.9446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN I 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 21340 Z= 0.286 Angle : 0.569 10.052 29025 Z= 0.280 Chirality : 0.043 0.231 3690 Planarity : 0.003 0.035 3492 Dihedral : 4.524 19.488 2637 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.76 (0.17), residues: 2415 helix: 1.42 (0.29), residues: 375 sheet: -0.42 (0.19), residues: 732 loop : -1.12 (0.17), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 2.701 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 79 average time/residue: 0.2818 time to fit residues: 39.3735 Evaluate side-chains 66 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1924 time to fit residues: 4.4793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 658 GLN B 650 GLN I 187 ASN L 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 21340 Z= 0.435 Angle : 0.665 8.635 29025 Z= 0.326 Chirality : 0.046 0.236 3690 Planarity : 0.004 0.036 3492 Dihedral : 4.822 20.594 2637 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.86 (0.17), residues: 2415 helix: 1.15 (0.29), residues: 375 sheet: -0.25 (0.20), residues: 687 loop : -1.27 (0.17), residues: 1353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 2.404 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 86 average time/residue: 0.2835 time to fit residues: 43.0820 Evaluate side-chains 76 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2008 time to fit residues: 7.3014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 231 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 66 HIS L 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 21340 Z= 0.132 Angle : 0.517 8.439 29025 Z= 0.253 Chirality : 0.041 0.250 3690 Planarity : 0.003 0.035 3492 Dihedral : 4.328 21.210 2637 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.61 (0.17), residues: 2415 helix: 1.66 (0.29), residues: 375 sheet: -0.33 (0.19), residues: 708 loop : -1.04 (0.17), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 2.417 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 0.2814 time to fit residues: 37.1590 Evaluate side-chains 66 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1826 time to fit residues: 3.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 157 optimal weight: 40.0000 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 21340 Z= 0.392 Angle : 0.635 7.466 29025 Z= 0.311 Chirality : 0.045 0.226 3690 Planarity : 0.004 0.035 3492 Dihedral : 4.628 21.027 2637 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.17), residues: 2415 helix: 1.23 (0.29), residues: 378 sheet: -0.22 (0.19), residues: 696 loop : -1.17 (0.17), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 2.464 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.2900 time to fit residues: 35.4655 Evaluate side-chains 68 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1924 time to fit residues: 4.9038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.2980 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 194 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21340 Z= 0.137 Angle : 0.517 7.735 29025 Z= 0.253 Chirality : 0.041 0.234 3690 Planarity : 0.003 0.035 3492 Dihedral : 4.310 21.309 2637 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.56 (0.17), residues: 2415 helix: 1.61 (0.29), residues: 378 sheet: -0.38 (0.19), residues: 741 loop : -0.95 (0.18), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 2.350 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.2914 time to fit residues: 34.8250 Evaluate side-chains 65 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1848 time to fit residues: 4.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 239 optimal weight: 0.0970 chunk 220 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 21340 Z= 0.295 Angle : 0.582 7.213 29025 Z= 0.284 Chirality : 0.043 0.214 3690 Planarity : 0.003 0.034 3492 Dihedral : 4.446 20.895 2637 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.66 (0.18), residues: 2415 helix: 1.50 (0.29), residues: 378 sheet: -0.41 (0.19), residues: 741 loop : -1.02 (0.18), residues: 1296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 3.337 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 0.3498 time to fit residues: 40.1171 Evaluate side-chains 62 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.0770 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.056083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.041511 restraints weight = 104700.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041791 restraints weight = 79151.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.041956 restraints weight = 62429.123| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 21340 Z= 0.151 Angle : 0.516 7.433 29025 Z= 0.252 Chirality : 0.041 0.212 3690 Planarity : 0.003 0.034 3492 Dihedral : 4.232 20.863 2637 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.18), residues: 2415 helix: 1.78 (0.29), residues: 375 sheet: -0.34 (0.19), residues: 741 loop : -0.85 (0.18), residues: 1299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2666.19 seconds wall clock time: 51 minutes 45.36 seconds (3105.36 seconds total)