Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 14:52:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy6_27776/08_2023/8dy6_27776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy6_27776/08_2023/8dy6_27776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy6_27776/08_2023/8dy6_27776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy6_27776/08_2023/8dy6_27776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy6_27776/08_2023/8dy6_27776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy6_27776/08_2023/8dy6_27776.pdb" } resolution = 4.32 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= 0.006 sd= 0.128 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 12918 2.51 5 N 3363 2.21 5 O 4365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 20778 Number of models: 1 Model: "" Number of chains: 54 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: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} 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: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 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: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} 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: 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: 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: "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: 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: "R" 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: "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: 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: "U" 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: "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 chiralities: 2 Chain: "W" 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: "X" 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: "Y" 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: "Z" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: "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: 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: "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: 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: "g" 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" 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: "j" 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" 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: "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: 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: 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: 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: 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: 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: "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: "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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.77, per 1000 atoms: 0.47 Number of scatterers: 20778 At special positions: 0 Unit cell: (159.84, 156.6, 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 4365 8.00 N 3363 7.00 C 12918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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 433 " distance=2.02 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 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " 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=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.02 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 433 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " 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=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 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 433 " 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 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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=2.04 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 U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA U 3 " - " MAN U 7 " " BMA W 3 " - " MAN W 5 " " BMA g 3 " - " MAN g 7 " " BMA i 3 " - " MAN i 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " NAG X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " NAG j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " 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 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 396 " " NAG A 703 " - " ASN A 234 " " 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 M 1 " - " ASN A 154 " " NAG N 1 " - " ASN E 154 " " NAG O 1 " - " ASN I 154 " " NAG P 1 " - " ASN E 442 " " NAG Q 1 " - " ASN E 301 " " NAG R 1 " - " ASN E 197 " " NAG S 1 " - " ASN E 392 " " NAG T 1 " - " ASN E 241 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 158 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 448 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 362 " " NAG b 1 " - " ASN A 442 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 392 " " NAG f 1 " - " ASN A 241 " " NAG g 1 " - " ASN A 332 " " NAG h 1 " - " ASN A 158 " " NAG j 1 " - " ASN A 448 " " NAG k 1 " - " ASN A 386 " " NAG l 1 " - " ASN A 362 " " NAG m 1 " - " ASN A 276 " " NAG n 1 " - " ASN A 339 " " NAG o 1 " - " ASN I 442 " " NAG p 1 " - " ASN I 301 " " 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 w 1 " - " ASN I 448 " " NAG x 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 362 " Time building additional restraints: 9.71 Conformation dependent library (CDL) restraints added in 2.6 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: 49 helices and 33 sheets defined 19.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.565A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.686A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.246A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.942A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.865A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.037A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.790A pdb=" N GLN C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.689A pdb=" N ALA D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 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 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.564A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 543 removed outlier: 3.630A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 4.135A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 4.126A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.830A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.509A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.589A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.632A 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 475 through 480 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 542 removed outlier: 4.222A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 597 removed outlier: 4.292A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN J 590 " --> pdb=" O TYR J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.788A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.608A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.748A pdb=" N GLN K 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.561A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.789A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.855A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.800A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 12 current: chain 'D' and resid 46 through 50 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 46 through 50 current: chain 'D' and resid 98 through 101 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.267A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.653A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.427A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.513A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.764A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.921A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 12 current: chain 'H' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 47 through 50 current: chain 'H' and resid 99 through 101 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AC5, first strand: chain 'I' and resid 494 through 498 removed outlier: 5.268A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.601A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.519A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AD1, first strand: chain 'I' and resid 201 through 203 removed outlier: 3.525A pdb=" N ILE I 424 " --> pdb=" O MET I 434 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 309 removed outlier: 6.909A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 413 through 420 current: chain 'I' and resid 465 through 470 Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 58 through 60 current: chain 'K' and resid 116 through 117 Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 46 through 50 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 50 current: chain 'L' and resid 98 through 101 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 18 through 23 517 hydrogen bonds defined for protein. 1416 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: 5.77 Time building geometry restraints manager: 10.38 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: 6275 1.34 - 1.46: 5236 1.46 - 1.58: 9510 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 21198 Sorted by residual: bond pdb=" C3 BMA O 3 " pdb=" O3 BMA O 3 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N ASN I 262 " pdb=" CA ASN I 262 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.72e+00 bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG e 2 " pdb=" O5 NAG e 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" C1 MAN U 4 " pdb=" O5 MAN U 4 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 21193 not shown) Histogram of bond angle deviations from ideal: 92.40 - 100.80: 32 100.80 - 109.19: 2160 109.19 - 117.58: 14543 117.58 - 125.97: 11658 125.97 - 134.36: 440 Bond angle restraints: 28833 Sorted by residual: angle pdb=" N ILE J 635 " pdb=" CA ILE J 635 " pdb=" C ILE J 635 " ideal model delta sigma weight residual 112.29 108.07 4.22 9.40e-01 1.13e+00 2.02e+01 angle pdb=" N ILE F 635 " pdb=" CA ILE F 635 " pdb=" C ILE F 635 " ideal model delta sigma weight residual 112.29 108.20 4.09 9.40e-01 1.13e+00 1.89e+01 angle pdb=" C TRP C 47 " pdb=" N MET C 48 " pdb=" CA MET C 48 " ideal model delta sigma weight residual 122.08 115.55 6.53 1.53e+00 4.27e-01 1.82e+01 angle pdb=" C LEU I 261 " pdb=" N ASN I 262 " pdb=" CA ASN I 262 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ASN E 276 " pdb=" N LEU E 277 " pdb=" CA LEU E 277 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 28828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 10578 17.64 - 35.29: 863 35.29 - 52.93: 171 52.93 - 70.57: 23 70.57 - 88.21: 26 Dihedral angle restraints: 11661 sinusoidal: 4605 harmonic: 7056 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 93.00 160.57 -67.57 1 1.00e+01 1.00e-02 5.94e+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 93.00 157.13 -64.13 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.42 -60.42 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 11658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2991 0.076 - 0.151: 551 0.151 - 0.227: 49 0.227 - 0.302: 22 0.302 - 0.378: 6 Chirality restraints: 3619 Sorted by residual: chirality pdb=" C1 NAG E 702 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 702 " pdb=" O5 NAG E 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN A 276 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C5 BMA v 3 " pdb=" C4 BMA v 3 " pdb=" C6 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 3616 not shown) Planarity restraints: 3538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 653 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C GLN F 653 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN F 653 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 654 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 646 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C LEU F 646 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU F 646 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU F 647 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 652 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C GLN F 652 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN F 652 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN F 653 " -0.014 2.00e-02 2.50e+03 ... (remaining 3535 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5210 2.79 - 3.32: 19098 3.32 - 3.85: 35670 3.85 - 4.37: 39146 4.37 - 4.90: 67020 Nonbonded interactions: 166144 Sorted by model distance: nonbonded pdb=" O ALA D 94 " pdb=" OG1 THR D 98 " model vdw 2.266 2.440 nonbonded pdb=" O ILE I 358 " pdb=" OG1 THR I 394 " model vdw 2.272 2.440 nonbonded pdb=" O MET I 369 " pdb=" OG1 THR I 373 " model vdw 2.282 2.440 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.282 2.440 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.284 2.440 ... (remaining 166139 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' and (resid 33 through 505 or resid 701 through 702)) selection = (chain 'E' and (resid 33 through 505 or resid 701 through 702)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' 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 'S' selection = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'l' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'U' selection = chain 'g' selection = chain 't' } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.670 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 50.450 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.300 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.006 0.075 21198 Z= 0.397 Angle : 0.972 11.229 28833 Z= 0.484 Chirality : 0.061 0.378 3619 Planarity : 0.006 0.048 3492 Dihedral : 13.748 88.213 7026 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % 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: -1.13 (0.16), residues: 2415 helix: -0.65 (0.24), residues: 408 sheet: -0.17 (0.20), residues: 636 loop : -1.04 (0.16), residues: 1371 *********************** 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 47 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 2.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3096 time to fit residues: 26.1755 Evaluate side-chains 46 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7301 ------------------------------------------------------------------------------- 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: 30.0000 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 0.3980 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 630 GLN E 428 GLN I 350 GLN ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 21198 Z= 0.243 Angle : 0.560 6.239 28833 Z= 0.281 Chirality : 0.041 0.276 3619 Planarity : 0.004 0.034 3492 Dihedral : 5.977 81.013 2640 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.23 % 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: -0.38 (0.17), residues: 2415 helix: 0.73 (0.27), residues: 396 sheet: -0.04 (0.20), residues: 636 loop : -0.61 (0.17), residues: 1383 *********************** 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 46 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 2.422 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3010 time to fit residues: 25.4960 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9844 ------------------------------------------------------------------------------- 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: 30.0000 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 0.0070 chunk 148 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 30.0000 chunk 235 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21198 Z= 0.184 Angle : 0.518 6.164 28833 Z= 0.259 Chirality : 0.041 0.292 3619 Planarity : 0.003 0.033 3492 Dihedral : 5.709 82.148 2640 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % 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: -0.17 (0.18), residues: 2415 helix: 1.14 (0.28), residues: 399 sheet: -0.03 (0.21), residues: 642 loop : -0.48 (0.17), residues: 1374 *********************** 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 46 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 2.315 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3025 time to fit residues: 25.1657 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0217 ------------------------------------------------------------------------------- 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: 8.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS E 103 GLN ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 21198 Z= 0.416 Angle : 0.712 7.835 28833 Z= 0.349 Chirality : 0.043 0.263 3619 Planarity : 0.004 0.034 3492 Dihedral : 6.080 83.976 2640 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer Outliers : 0.05 % 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: -0.48 (0.18), residues: 2415 helix: 0.80 (0.27), residues: 420 sheet: -0.41 (0.20), residues: 666 loop : -0.57 (0.18), residues: 1329 *********************** 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 46 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 2.384 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.3123 time to fit residues: 26.0309 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6189 ------------------------------------------------------------------------------- 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: 5.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 21198 Z= 0.254 Angle : 0.584 7.562 28833 Z= 0.288 Chirality : 0.042 0.273 3619 Planarity : 0.003 0.034 3492 Dihedral : 5.867 85.363 2640 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % 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: -0.32 (0.18), residues: 2415 helix: 1.02 (0.27), residues: 420 sheet: -0.34 (0.20), residues: 666 loop : -0.47 (0.18), residues: 1329 *********************** 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 47 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 2.288 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3047 time to fit residues: 25.7731 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1942 ------------------------------------------------------------------------------- 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: 20.0000 chunk 208 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 232 optimal weight: 0.4980 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 40.0000 chunk 121 optimal weight: 9.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 21198 Z= 0.266 Angle : 0.588 6.967 28833 Z= 0.288 Chirality : 0.042 0.273 3619 Planarity : 0.003 0.032 3492 Dihedral : 5.806 86.832 2640 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % 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: -0.27 (0.18), residues: 2415 helix: 1.08 (0.27), residues: 420 sheet: -0.32 (0.20), residues: 666 loop : -0.44 (0.18), residues: 1329 *********************** 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 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3033 time to fit residues: 25.1224 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4458 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 106 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 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 21198 Z= 0.184 Angle : 0.542 6.521 28833 Z= 0.266 Chirality : 0.041 0.277 3619 Planarity : 0.003 0.032 3492 Dihedral : 5.673 88.207 2640 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.73 % 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: -0.16 (0.18), residues: 2415 helix: 1.25 (0.28), residues: 420 sheet: -0.37 (0.21), residues: 642 loop : -0.33 (0.18), residues: 1353 *********************** 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 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.385 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2939 time to fit residues: 24.3746 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8302 ------------------------------------------------------------------------------- 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: 5.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 0.0470 chunk 181 optimal weight: 0.0770 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN ** J 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21198 Z= 0.122 Angle : 0.517 10.144 28833 Z= 0.253 Chirality : 0.042 0.282 3619 Planarity : 0.003 0.031 3492 Dihedral : 5.446 89.937 2640 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.06 (0.18), residues: 2415 helix: 1.74 (0.29), residues: 384 sheet: -0.21 (0.21), residues: 654 loop : -0.26 (0.18), residues: 1377 *********************** 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 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.313 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3013 time to fit residues: 24.5775 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9274 ------------------------------------------------------------------------------- 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: 7.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 0.0870 chunk 215 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21198 Z= 0.216 Angle : 0.545 8.444 28833 Z= 0.267 Chirality : 0.041 0.275 3619 Planarity : 0.003 0.030 3492 Dihedral : 5.439 88.003 2640 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.73 % 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: 0.02 (0.18), residues: 2415 helix: 1.56 (0.29), residues: 402 sheet: -0.27 (0.20), residues: 675 loop : -0.24 (0.18), residues: 1338 *********************** 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 46 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 2.427 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3163 time to fit residues: 26.4541 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1710 ------------------------------------------------------------------------------- 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: 4.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 158 optimal weight: 40.0000 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 21198 Z= 0.236 Angle : 0.566 8.521 28833 Z= 0.277 Chirality : 0.041 0.271 3619 Planarity : 0.003 0.031 3492 Dihedral : 5.500 85.228 2640 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % 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: -0.01 (0.18), residues: 2415 helix: 1.52 (0.28), residues: 402 sheet: -0.28 (0.20), residues: 669 loop : -0.26 (0.18), residues: 1344 ********************** 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 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.483 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3116 time to fit residues: 25.5728 Evaluate side-chains 45 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0384 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 190 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.024520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.019073 restraints weight = 324672.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.019607 restraints weight = 196143.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.019961 restraints weight = 143653.130| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21198 Z= 0.159 Angle : 0.523 8.803 28833 Z= 0.256 Chirality : 0.041 0.277 3619 Planarity : 0.003 0.030 3492 Dihedral : 5.354 83.317 2640 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % 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: 0.08 (0.18), residues: 2415 helix: 1.70 (0.29), residues: 387 sheet: -0.27 (0.20), residues: 726 loop : -0.16 (0.18), residues: 1302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.12 seconds wall clock time: 48 minutes 33.45 seconds (2913.45 seconds total)