Starting phenix.real_space_refine on Mon Mar 18 01:52:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo3_21258/03_2024/6vo3_21258.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo3_21258/03_2024/6vo3_21258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo3_21258/03_2024/6vo3_21258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo3_21258/03_2024/6vo3_21258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo3_21258/03_2024/6vo3_21258.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo3_21258/03_2024/6vo3_21258.pdb" } resolution = 4.25 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= 0.002 sd= 0.049 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 120 5.16 5 C 12300 2.51 5 N 3300 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19554 Number of models: 1 Model: "" Number of chains: 39 Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "A" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "E" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "D" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "F" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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 dihedrals: 9 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.09, per 1000 atoms: 0.52 Number of scatterers: 19554 At special positions: 0 Unit cell: (144.1, 148.03, 116.59, 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 120 16.00 O 3834 8.00 N 3300 7.00 C 12300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.13 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.13 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.13 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA U 3 " - " MAN U 5 " " BMA b 3 " - " MAN b 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 614 " - " ASN A 396 " " NAG A 615 " - " ASN A 448 " " NAG A 619 " - " ASN A 463 " " NAG A 622 " - " ASN A 234 " " NAG A 623 " - " ASN A 197 " " NAG B 701 " - " ASN B 625 " " NAG C 614 " - " ASN C 396 " " NAG C 615 " - " ASN C 448 " " NAG C 619 " - " ASN C 463 " " NAG C 622 " - " ASN C 234 " " NAG C 623 " - " ASN C 197 " " NAG D 614 " - " ASN D 396 " " NAG D 615 " - " ASN D 448 " " NAG D 619 " - " ASN D 463 " " NAG D 622 " - " ASN D 234 " " NAG D 623 " - " ASN D 197 " " NAG E 701 " - " ASN E 625 " " NAG F 701 " - " ASN F 625 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN A 362 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 276 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 392 " " NAG X 1 " - " ASN C 362 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 88 " " NAG a 1 " - " ASN D 262 " " NAG b 1 " - " ASN D 276 " " NAG c 1 " - " ASN D 386 " " NAG d 1 " - " ASN D 392 " " NAG e 1 " - " ASN D 362 " " NAG f 1 " - " ASN D 241 " " NAG g 1 " - " ASN D 88 " Time building additional restraints: 7.62 Conformation dependent library (CDL) restraints added in 3.0 seconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 24.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'H' and resid 25 through 31 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.206A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.560A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 651 through 664 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.206A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.561A pdb=" N ILE E 622 " --> pdb=" O SER E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU E 634 " --> pdb=" O GLU E 630 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 651 Processing helix chain 'E' and resid 651 through 664 Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.207A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.560A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG F 633 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 651 Processing helix chain 'F' and resid 651 through 664 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.688A pdb=" N CYS H 92 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.160A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.688A pdb=" N CYS G 92 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.950A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.950A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.161A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.687A pdb=" N CYS I 92 " --> pdb=" O GLY I 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AE1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS D 54 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE4, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.161A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.786A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.786A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 315 through 323A removed outlier: 7.393A pdb=" N TRP D 316 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 309 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 322 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 315 through 323A removed outlier: 7.393A pdb=" N TRP D 316 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 309 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 322 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4975 1.33 - 1.47: 6369 1.47 - 1.61: 8444 1.61 - 1.74: 12 1.74 - 1.88: 159 Bond restraints: 19959 Sorted by residual: bond pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.75e+01 bond pdb=" CB CYS J 88 " pdb=" SG CYS J 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.75e+01 bond pdb=" CB CYS K 88 " pdb=" SG CYS K 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.74e+01 bond pdb=" CB HIS C 330 " pdb=" CG HIS C 330 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.49e+01 ... (remaining 19954 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.35: 556 105.35 - 112.69: 10124 112.69 - 120.03: 8018 120.03 - 127.37: 8108 127.37 - 134.71: 266 Bond angle restraints: 27072 Sorted by residual: angle pdb=" CA PHE A 53 " pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 113.80 121.92 -8.12 1.00e+00 1.00e+00 6.59e+01 angle pdb=" CA PHE D 53 " pdb=" CB PHE D 53 " pdb=" CG PHE D 53 " ideal model delta sigma weight residual 113.80 121.91 -8.11 1.00e+00 1.00e+00 6.57e+01 angle pdb=" CA PHE C 53 " pdb=" CB PHE C 53 " pdb=" CG PHE C 53 " ideal model delta sigma weight residual 113.80 121.90 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 108.17 119.06 -10.89 1.40e+00 5.10e-01 6.05e+01 angle pdb=" N ILE C 181 " pdb=" CA ILE C 181 " pdb=" C ILE C 181 " ideal model delta sigma weight residual 108.17 119.06 -10.89 1.40e+00 5.10e-01 6.05e+01 ... (remaining 27067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 12256 21.68 - 43.35: 437 43.35 - 65.03: 135 65.03 - 86.70: 66 86.70 - 108.38: 57 Dihedral angle restraints: 12951 sinusoidal: 6237 harmonic: 6714 Sorted by residual: dihedral pdb=" C LEU E 537 " pdb=" N LEU E 537 " pdb=" CA LEU E 537 " pdb=" CB LEU E 537 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU F 537 " pdb=" N LEU F 537 " pdb=" CA LEU F 537 " pdb=" CB LEU F 537 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C LEU B 537 " pdb=" N LEU B 537 " pdb=" CA LEU B 537 " pdb=" CB LEU B 537 " ideal model delta harmonic sigma weight residual -122.60 -112.30 -10.30 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 12948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2392 0.113 - 0.226: 729 0.226 - 0.339: 101 0.339 - 0.452: 3 0.452 - 0.565: 12 Chirality restraints: 3237 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.33e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.26e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.18e+01 ... (remaining 3234 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.088 2.00e-02 2.50e+03 7.24e-02 6.55e+01 pdb=" C7 NAG T 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.088 2.00e-02 2.50e+03 7.24e-02 6.54e+01 pdb=" C7 NAG a 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.088 2.00e-02 2.50e+03 7.23e-02 6.54e+01 pdb=" C7 NAG M 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.017 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 7888 2.89 - 3.39: 17911 3.39 - 3.89: 34105 3.89 - 4.40: 39417 4.40 - 4.90: 62034 Nonbonded interactions: 161355 Sorted by model distance: nonbonded pdb=" N ASP C 57 " pdb=" OD1 ASP C 57 " model vdw 2.385 2.520 nonbonded pdb=" N ASP A 57 " pdb=" OD1 ASP A 57 " model vdw 2.385 2.520 nonbonded pdb=" N ASP D 57 " pdb=" OD1 ASP D 57 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP H 27 " pdb=" NZ LYS C 207 " model vdw 2.387 2.520 nonbonded pdb=" NZ LYS A 207 " pdb=" OD1 ASP I 27 " model vdw 2.387 2.520 ... (remaining 161350 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.580 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 50.440 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.019 0.173 19959 Z= 1.242 Angle : 1.841 10.890 27072 Z= 1.172 Chirality : 0.106 0.565 3237 Planarity : 0.009 0.072 3336 Dihedral : 15.585 108.378 8505 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.82 % Favored : 95.66 % Rotamer: Outliers : 0.44 % Allowed : 1.32 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.21 (0.17), residues: 2280 helix: -0.25 (0.23), residues: 429 sheet: 0.78 (0.19), residues: 642 loop : 0.05 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.011 TRP B 571 HIS 0.016 0.004 HIS A 374 PHE 0.032 0.006 PHE D 53 TYR 0.042 0.009 TYR C 486 ARG 0.006 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 683 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8039 (mt) cc_final: 0.7023 (mt) REVERT: H 36 TRP cc_start: 0.9324 (m100) cc_final: 0.8905 (m100) REVERT: H 72 ASP cc_start: 0.7945 (t0) cc_final: 0.7462 (t0) REVERT: H 75 LEU cc_start: 0.9001 (mt) cc_final: 0.8752 (mt) REVERT: H 80 MET cc_start: 0.8778 (ttp) cc_final: 0.8493 (ttt) REVERT: H 81 ASP cc_start: 0.7892 (m-30) cc_final: 0.7628 (p0) REVERT: L 86 TYR cc_start: 0.8245 (m-80) cc_final: 0.7760 (m-10) REVERT: A 69 TRP cc_start: 0.7677 (m-90) cc_final: 0.6700 (m-90) REVERT: A 95 MET cc_start: 0.8697 (ptm) cc_final: 0.8492 (ptm) REVERT: A 195 ASN cc_start: 0.7968 (m-40) cc_final: 0.7672 (m110) REVERT: A 434 MET cc_start: 0.8486 (ttp) cc_final: 0.7924 (tmm) REVERT: A 494 LEU cc_start: 0.8870 (mt) cc_final: 0.8521 (pp) REVERT: B 622 ILE cc_start: 0.8882 (pt) cc_final: 0.8528 (mp) REVERT: G 4 LEU cc_start: 0.7919 (mt) cc_final: 0.7130 (mt) REVERT: G 13 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8480 (mmmt) REVERT: G 36 TRP cc_start: 0.9353 (m100) cc_final: 0.9024 (m100) REVERT: G 72 ASP cc_start: 0.7949 (t0) cc_final: 0.7646 (t0) REVERT: G 80 MET cc_start: 0.8817 (ttp) cc_final: 0.6552 (ttp) REVERT: G 81 ASP cc_start: 0.8264 (m-30) cc_final: 0.7909 (p0) REVERT: J 86 TYR cc_start: 0.8331 (m-80) cc_final: 0.7812 (m-10) REVERT: J 102 THR cc_start: 0.8060 (p) cc_final: 0.7836 (m) REVERT: C 69 TRP cc_start: 0.7949 (m-90) cc_final: 0.7479 (m-90) REVERT: C 181 ILE cc_start: 0.8666 (mt) cc_final: 0.8423 (pt) REVERT: C 195 ASN cc_start: 0.8151 (m-40) cc_final: 0.7850 (m110) REVERT: C 475 MET cc_start: 0.8325 (mmt) cc_final: 0.7992 (mmt) REVERT: C 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8603 (mt) REVERT: E 658 GLN cc_start: 0.8204 (tp40) cc_final: 0.8002 (tp40) REVERT: I 4 LEU cc_start: 0.8395 (mt) cc_final: 0.7691 (mt) REVERT: I 13 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8655 (mmmt) REVERT: I 80 MET cc_start: 0.8728 (ttp) cc_final: 0.8138 (ttp) REVERT: I 81 ASP cc_start: 0.8262 (m-30) cc_final: 0.7859 (p0) REVERT: I 100 GLN cc_start: 0.5169 (mt0) cc_final: 0.4708 (mm110) REVERT: K 86 TYR cc_start: 0.8272 (m-80) cc_final: 0.7705 (m-10) REVERT: K 104 LEU cc_start: 0.8265 (mt) cc_final: 0.8018 (mt) REVERT: D 69 TRP cc_start: 0.8116 (m-90) cc_final: 0.7187 (m-90) REVERT: D 181 ILE cc_start: 0.8570 (mt) cc_final: 0.8331 (pt) REVERT: D 475 MET cc_start: 0.8386 (mmt) cc_final: 0.8137 (mmt) REVERT: D 494 LEU cc_start: 0.8740 (mt) cc_final: 0.8479 (mp) REVERT: F 576 LEU cc_start: 0.8748 (tp) cc_final: 0.8539 (tt) outliers start: 9 outliers final: 6 residues processed: 692 average time/residue: 0.3573 time to fit residues: 355.2409 Evaluate side-chains 340 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 334 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS A 105 HIS A 195 ASN A 229 ASN A 377 ASN A 425 ASN B 590 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 105 HIS C 195 ASN C 229 ASN C 425 ASN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN D 72 HIS D 105 HIS D 229 ASN F 590 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19959 Z= 0.285 Angle : 0.885 13.897 27072 Z= 0.455 Chirality : 0.053 0.339 3237 Planarity : 0.005 0.061 3336 Dihedral : 12.593 84.770 4098 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.09 % Favored : 94.08 % Rotamer: Outliers : 0.20 % Allowed : 2.74 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.14 (0.17), residues: 2280 helix: 0.57 (0.24), residues: 447 sheet: 0.68 (0.19), residues: 648 loop : -0.37 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 112 HIS 0.006 0.001 HIS D 330 PHE 0.030 0.003 PHE G 76 TYR 0.051 0.002 TYR E 643 ARG 0.009 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 480 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8533 (mt) cc_final: 0.7157 (mt) REVERT: H 28 ILE cc_start: 0.9548 (mm) cc_final: 0.9169 (mm) REVERT: H 34 LEU cc_start: 0.9136 (mt) cc_final: 0.8887 (mt) REVERT: H 81 ASP cc_start: 0.8019 (m-30) cc_final: 0.7718 (p0) REVERT: H 108 LEU cc_start: 0.9104 (tp) cc_final: 0.8827 (tp) REVERT: L 47 LEU cc_start: 0.8690 (mm) cc_final: 0.8336 (pp) REVERT: L 86 TYR cc_start: 0.8239 (m-80) cc_final: 0.7906 (m-10) REVERT: L 97 PHE cc_start: 0.8435 (m-10) cc_final: 0.8152 (m-80) REVERT: A 342 LEU cc_start: 0.9325 (mp) cc_final: 0.9106 (mm) REVERT: B 584 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 628 TRP cc_start: 0.8036 (m100) cc_final: 0.7498 (m100) REVERT: B 630 GLU cc_start: 0.8443 (pt0) cc_final: 0.8142 (pt0) REVERT: B 662 GLU cc_start: 0.7691 (tt0) cc_final: 0.7357 (tt0) REVERT: G 34 LEU cc_start: 0.8954 (mt) cc_final: 0.8581 (mt) REVERT: G 36 TRP cc_start: 0.9337 (m100) cc_final: 0.8830 (m-10) REVERT: G 108 LEU cc_start: 0.9158 (tp) cc_final: 0.8947 (tp) REVERT: J 86 TYR cc_start: 0.8482 (m-80) cc_final: 0.8120 (m-10) REVERT: C 256 SER cc_start: 0.8298 (p) cc_final: 0.8074 (m) REVERT: E 530 MET cc_start: 0.7406 (ptm) cc_final: 0.6662 (ptm) REVERT: E 546 SER cc_start: 0.7977 (t) cc_final: 0.7515 (p) REVERT: E 662 GLU cc_start: 0.8336 (pt0) cc_final: 0.8064 (tt0) REVERT: I 4 LEU cc_start: 0.8118 (mt) cc_final: 0.7882 (mt) REVERT: I 27 ASP cc_start: 0.9462 (p0) cc_final: 0.9255 (p0) REVERT: I 81 ASP cc_start: 0.8303 (m-30) cc_final: 0.7784 (p0) REVERT: I 100 GLN cc_start: 0.5329 (mt0) cc_final: 0.4453 (mm110) REVERT: I 108 LEU cc_start: 0.8938 (tp) cc_final: 0.8716 (tp) REVERT: K 33 MET cc_start: 0.7668 (ptp) cc_final: 0.7240 (tmm) REVERT: K 47 LEU cc_start: 0.8925 (mm) cc_final: 0.8498 (pp) REVERT: K 86 TYR cc_start: 0.7984 (m-80) cc_final: 0.7749 (m-10) REVERT: D 316 TRP cc_start: 0.5692 (m-90) cc_final: 0.5446 (m-90) REVERT: D 475 MET cc_start: 0.8264 (mmt) cc_final: 0.8013 (mmt) REVERT: F 530 MET cc_start: 0.7210 (ptt) cc_final: 0.6840 (ptt) REVERT: F 574 LYS cc_start: 0.8957 (mttt) cc_final: 0.8675 (ttmm) REVERT: F 628 TRP cc_start: 0.7493 (m100) cc_final: 0.6997 (m100) outliers start: 4 outliers final: 0 residues processed: 482 average time/residue: 0.3255 time to fit residues: 234.1537 Evaluate side-chains 309 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 0.0970 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN C 302 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19959 Z= 0.250 Angle : 0.779 9.697 27072 Z= 0.395 Chirality : 0.051 0.370 3237 Planarity : 0.005 0.063 3336 Dihedral : 9.838 73.239 4098 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.70 % Favored : 93.77 % Rotamer: Outliers : 0.29 % Allowed : 2.93 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.13 (0.17), residues: 2280 helix: 0.75 (0.24), residues: 444 sheet: 0.68 (0.20), residues: 624 loop : -0.44 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 479 HIS 0.006 0.001 HIS D 105 PHE 0.033 0.002 PHE D 391 TYR 0.021 0.002 TYR E 643 ARG 0.013 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 410 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ASP cc_start: 0.9398 (p0) cc_final: 0.9114 (p0) REVERT: H 28 ILE cc_start: 0.9453 (mm) cc_final: 0.9106 (mm) REVERT: H 46 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8161 (mm-30) REVERT: H 72 ASP cc_start: 0.7906 (t0) cc_final: 0.7517 (t0) REVERT: H 80 MET cc_start: 0.8958 (ttp) cc_final: 0.7758 (ttp) REVERT: H 108 LEU cc_start: 0.9134 (tp) cc_final: 0.8818 (tp) REVERT: L 4 LEU cc_start: 0.8674 (tp) cc_final: 0.8346 (tp) REVERT: L 33 MET cc_start: 0.7955 (pmm) cc_final: 0.7672 (pmm) REVERT: L 47 LEU cc_start: 0.8601 (mm) cc_final: 0.8303 (pp) REVERT: L 86 TYR cc_start: 0.8224 (m-80) cc_final: 0.7949 (m-10) REVERT: L 97 PHE cc_start: 0.8560 (m-10) cc_final: 0.8360 (m-80) REVERT: A 373 MET cc_start: 0.8578 (mtp) cc_final: 0.8171 (mmm) REVERT: B 584 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8555 (tm-30) REVERT: B 588 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8689 (tpp80) REVERT: B 626 MET cc_start: 0.6974 (tpp) cc_final: 0.6170 (tpp) REVERT: B 628 TRP cc_start: 0.8350 (m100) cc_final: 0.7989 (m100) REVERT: B 647 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: G 34 LEU cc_start: 0.8909 (mt) cc_final: 0.8527 (mt) REVERT: G 36 TRP cc_start: 0.9272 (m100) cc_final: 0.8785 (m-10) REVERT: G 46 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7842 (mm-30) REVERT: G 72 ASP cc_start: 0.8344 (t0) cc_final: 0.8123 (t0) REVERT: G 81 ASP cc_start: 0.7380 (p0) cc_final: 0.7142 (p0) REVERT: G 108 LEU cc_start: 0.9226 (tp) cc_final: 0.8951 (tp) REVERT: J 33 MET cc_start: 0.7981 (pmm) cc_final: 0.7751 (pmm) REVERT: C 373 MET cc_start: 0.8368 (mtp) cc_final: 0.7815 (mmm) REVERT: C 420 ILE cc_start: 0.8846 (mm) cc_final: 0.8590 (mm) REVERT: E 546 SER cc_start: 0.8051 (t) cc_final: 0.7830 (p) REVERT: E 588 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8318 (tpp80) REVERT: E 619 LEU cc_start: 0.9141 (tp) cc_final: 0.8934 (tp) REVERT: I 81 ASP cc_start: 0.7985 (m-30) cc_final: 0.7719 (p0) REVERT: I 100 GLN cc_start: 0.5561 (mt0) cc_final: 0.4663 (mp10) REVERT: I 108 LEU cc_start: 0.9022 (tp) cc_final: 0.8686 (tp) REVERT: K 33 MET cc_start: 0.7463 (ptp) cc_final: 0.6934 (tmm) REVERT: D 104 MET cc_start: 0.8888 (mmp) cc_final: 0.8480 (mmp) REVERT: D 108 ILE cc_start: 0.9524 (pt) cc_final: 0.9230 (pt) REVERT: D 373 MET cc_start: 0.8474 (mtp) cc_final: 0.7775 (mmm) REVERT: D 420 ILE cc_start: 0.8789 (mm) cc_final: 0.8558 (mm) REVERT: D 492 GLU cc_start: 0.8891 (tp30) cc_final: 0.8287 (tm-30) REVERT: F 628 TRP cc_start: 0.7846 (m100) cc_final: 0.7514 (m100) outliers start: 6 outliers final: 1 residues processed: 414 average time/residue: 0.3398 time to fit residues: 209.6411 Evaluate side-chains 272 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN B 543 GLN B 590 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19959 Z= 0.291 Angle : 0.769 9.519 27072 Z= 0.391 Chirality : 0.050 0.344 3237 Planarity : 0.004 0.048 3336 Dihedral : 8.665 62.315 4098 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.05 % Favored : 93.42 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.17), residues: 2280 helix: 0.76 (0.24), residues: 447 sheet: 0.52 (0.19), residues: 642 loop : -0.57 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 479 HIS 0.005 0.001 HIS G 79 PHE 0.026 0.002 PHE A 391 TYR 0.019 0.002 TYR F 638 ARG 0.012 0.001 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8462 (mt) cc_final: 0.8201 (mt) REVERT: H 27 ASP cc_start: 0.9343 (p0) cc_final: 0.9006 (p0) REVERT: H 28 ILE cc_start: 0.9329 (mm) cc_final: 0.9114 (mm) REVERT: H 46 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7984 (mm-30) REVERT: H 72 ASP cc_start: 0.7748 (t0) cc_final: 0.7486 (t0) REVERT: H 75 LEU cc_start: 0.8944 (mt) cc_final: 0.8233 (mt) REVERT: H 108 LEU cc_start: 0.9154 (tp) cc_final: 0.8905 (tp) REVERT: L 4 LEU cc_start: 0.8745 (tp) cc_final: 0.8359 (tp) REVERT: L 30 TYR cc_start: 0.7997 (m-80) cc_final: 0.6864 (m-80) REVERT: L 47 LEU cc_start: 0.8807 (mm) cc_final: 0.8505 (pp) REVERT: L 75 ILE cc_start: 0.8830 (mm) cc_final: 0.8583 (mp) REVERT: L 86 TYR cc_start: 0.8133 (m-80) cc_final: 0.7713 (m-10) REVERT: L 96 GLU cc_start: 0.8910 (pm20) cc_final: 0.8086 (pm20) REVERT: L 97 PHE cc_start: 0.8674 (m-10) cc_final: 0.7723 (m-10) REVERT: A 342 LEU cc_start: 0.9405 (mp) cc_final: 0.9182 (mm) REVERT: A 373 MET cc_start: 0.8649 (mtp) cc_final: 0.8102 (mmm) REVERT: B 662 GLU cc_start: 0.7669 (tt0) cc_final: 0.7271 (tt0) REVERT: G 27 ASP cc_start: 0.9103 (p0) cc_final: 0.8721 (p0) REVERT: G 28 ILE cc_start: 0.9115 (mt) cc_final: 0.8866 (mm) REVERT: G 34 LEU cc_start: 0.8786 (mt) cc_final: 0.8420 (mt) REVERT: G 36 TRP cc_start: 0.9174 (m100) cc_final: 0.8609 (m-10) REVERT: G 46 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7867 (mm-30) REVERT: G 72 ASP cc_start: 0.8292 (t0) cc_final: 0.7828 (t0) REVERT: G 75 LEU cc_start: 0.9083 (mt) cc_final: 0.8696 (mt) REVERT: G 97 PHE cc_start: 0.6072 (m-80) cc_final: 0.5631 (m-80) REVERT: G 108 LEU cc_start: 0.9275 (tp) cc_final: 0.9032 (tp) REVERT: J 33 MET cc_start: 0.8089 (pmm) cc_final: 0.7839 (pmm) REVERT: C 420 ILE cc_start: 0.8720 (mm) cc_final: 0.8496 (mm) REVERT: E 546 SER cc_start: 0.8231 (t) cc_final: 0.7928 (p) REVERT: E 655 LYS cc_start: 0.9064 (pttp) cc_final: 0.8659 (pttm) REVERT: E 659 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8565 (mm-30) REVERT: E 662 GLU cc_start: 0.7985 (pt0) cc_final: 0.7345 (pt0) REVERT: I 46 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8224 (mp0) REVERT: I 97 PHE cc_start: 0.6634 (m-80) cc_final: 0.5918 (m-80) REVERT: I 100 GLN cc_start: 0.5766 (mt0) cc_final: 0.5089 (mm110) REVERT: I 108 LEU cc_start: 0.9092 (tp) cc_final: 0.8760 (tp) REVERT: K 47 LEU cc_start: 0.8838 (pp) cc_final: 0.8608 (mp) REVERT: D 104 MET cc_start: 0.8859 (mmp) cc_final: 0.8517 (mmt) REVERT: D 373 MET cc_start: 0.8595 (mtp) cc_final: 0.7798 (mmm) REVERT: D 420 ILE cc_start: 0.8796 (mm) cc_final: 0.8563 (mm) REVERT: D 492 GLU cc_start: 0.8919 (tp30) cc_final: 0.8656 (tp30) REVERT: F 530 MET cc_start: 0.7446 (ptm) cc_final: 0.7202 (ptm) REVERT: F 628 TRP cc_start: 0.8198 (m100) cc_final: 0.6900 (m100) REVERT: F 647 GLU cc_start: 0.8473 (pm20) cc_final: 0.8122 (pm20) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3360 time to fit residues: 187.6580 Evaluate side-chains 268 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 79 HIS ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS I 95 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 19959 Z= 0.522 Angle : 0.943 12.932 27072 Z= 0.483 Chirality : 0.053 0.342 3237 Planarity : 0.006 0.063 3336 Dihedral : 8.929 57.174 4098 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.72 % Favored : 91.80 % Rotamer: Outliers : 0.15 % Allowed : 2.44 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.17), residues: 2280 helix: 0.01 (0.24), residues: 426 sheet: 0.10 (0.19), residues: 684 loop : -0.83 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP F 596 HIS 0.008 0.002 HIS I 35A PHE 0.028 0.003 PHE D 53 TYR 0.025 0.003 TYR D 217 ARG 0.009 0.001 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 322 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8879 (mt) cc_final: 0.8612 (mt) REVERT: H 13 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8326 (mmmm) REVERT: H 27 ASP cc_start: 0.9252 (p0) cc_final: 0.8883 (p0) REVERT: H 28 ILE cc_start: 0.9216 (mm) cc_final: 0.9010 (mm) REVERT: H 46 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8360 (mm-30) REVERT: H 72 ASP cc_start: 0.7979 (t0) cc_final: 0.7628 (t0) REVERT: H 75 LEU cc_start: 0.9081 (mt) cc_final: 0.8761 (mt) REVERT: H 76 PHE cc_start: 0.8509 (m-10) cc_final: 0.7743 (m-10) REVERT: H 108 LEU cc_start: 0.9283 (tp) cc_final: 0.8958 (tp) REVERT: L 47 LEU cc_start: 0.8801 (mm) cc_final: 0.8464 (pp) REVERT: L 96 GLU cc_start: 0.8910 (pm20) cc_final: 0.8290 (pm20) REVERT: L 97 PHE cc_start: 0.8894 (m-10) cc_final: 0.7941 (m-10) REVERT: A 95 MET cc_start: 0.9273 (ppp) cc_final: 0.8649 (ppp) REVERT: A 308 HIS cc_start: 0.8215 (m90) cc_final: 0.7887 (m90) REVERT: B 584 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8708 (tm-30) REVERT: B 588 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8839 (tpp80) REVERT: B 647 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: G 27 ASP cc_start: 0.9350 (p0) cc_final: 0.8954 (p0) REVERT: G 34 LEU cc_start: 0.8874 (mt) cc_final: 0.8587 (mt) REVERT: G 46 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8107 (mm-30) REVERT: G 72 ASP cc_start: 0.8411 (t0) cc_final: 0.8073 (t0) REVERT: G 74 ASP cc_start: 0.8424 (p0) cc_final: 0.7954 (p0) REVERT: G 75 LEU cc_start: 0.9298 (mt) cc_final: 0.8717 (mt) REVERT: G 108 LEU cc_start: 0.9450 (tp) cc_final: 0.9151 (tp) REVERT: J 30 TYR cc_start: 0.7835 (m-80) cc_final: 0.7631 (m-80) REVERT: C 95 MET cc_start: 0.9262 (ppp) cc_final: 0.8754 (ppp) REVERT: C 104 MET cc_start: 0.9185 (mmt) cc_final: 0.8844 (mmt) REVERT: E 575 GLN cc_start: 0.8808 (pp30) cc_final: 0.8233 (pp30) REVERT: E 630 GLU cc_start: 0.8865 (pt0) cc_final: 0.8291 (pt0) REVERT: I 13 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8609 (mmmm) REVERT: I 46 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8108 (mm-30) REVERT: I 108 LEU cc_start: 0.9101 (tp) cc_final: 0.8754 (tp) REVERT: D 95 MET cc_start: 0.9225 (ppp) cc_final: 0.8916 (ppp) REVERT: D 195 ASN cc_start: 0.8611 (m110) cc_final: 0.8279 (m-40) REVERT: D 373 MET cc_start: 0.8812 (mtp) cc_final: 0.8327 (mmm) REVERT: F 588 ARG cc_start: 0.9090 (ttm170) cc_final: 0.8819 (ttm170) REVERT: F 628 TRP cc_start: 0.8694 (m100) cc_final: 0.7906 (m100) outliers start: 3 outliers final: 0 residues processed: 324 average time/residue: 0.3135 time to fit residues: 153.6155 Evaluate side-chains 234 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN B 543 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN F 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19959 Z= 0.231 Angle : 0.739 12.104 27072 Z= 0.378 Chirality : 0.050 0.354 3237 Planarity : 0.004 0.065 3336 Dihedral : 8.352 54.623 4098 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.23 % Favored : 93.46 % Rotamer: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.40 (0.17), residues: 2280 helix: 0.34 (0.25), residues: 420 sheet: 0.34 (0.19), residues: 657 loop : -0.80 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 479 HIS 0.005 0.001 HIS I 79 PHE 0.040 0.002 PHE H 76 TYR 0.023 0.002 TYR F 638 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7967 (t0) cc_final: 0.7629 (t0) REVERT: H 75 LEU cc_start: 0.9087 (mt) cc_final: 0.8693 (mt) REVERT: H 108 LEU cc_start: 0.9263 (tp) cc_final: 0.8815 (tp) REVERT: H 109 ILE cc_start: 0.9458 (mm) cc_final: 0.9164 (mt) REVERT: L 4 LEU cc_start: 0.8710 (tp) cc_final: 0.8420 (tp) REVERT: L 96 GLU cc_start: 0.8842 (pm20) cc_final: 0.8168 (pm20) REVERT: L 97 PHE cc_start: 0.8640 (m-10) cc_final: 0.7706 (m-10) REVERT: A 95 MET cc_start: 0.9181 (ppp) cc_final: 0.8831 (ppp) REVERT: A 373 MET cc_start: 0.8806 (mtp) cc_final: 0.8017 (tpp) REVERT: B 575 GLN cc_start: 0.8716 (pp30) cc_final: 0.7592 (pp30) REVERT: B 584 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8611 (tm-30) REVERT: B 588 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8803 (tpp80) REVERT: B 596 TRP cc_start: 0.8662 (m-10) cc_final: 0.8413 (m-90) REVERT: B 628 TRP cc_start: 0.8333 (m100) cc_final: 0.7547 (m100) REVERT: B 630 GLU cc_start: 0.8685 (pt0) cc_final: 0.8221 (pt0) REVERT: G 27 ASP cc_start: 0.9054 (p0) cc_final: 0.8666 (p0) REVERT: G 28 ILE cc_start: 0.9100 (mt) cc_final: 0.8471 (mt) REVERT: G 34 LEU cc_start: 0.8786 (mt) cc_final: 0.8444 (mt) REVERT: G 36 TRP cc_start: 0.9045 (m100) cc_final: 0.8561 (m-10) REVERT: G 46 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8051 (mm-30) REVERT: G 72 ASP cc_start: 0.8247 (t0) cc_final: 0.7978 (t0) REVERT: G 74 ASP cc_start: 0.8566 (p0) cc_final: 0.8356 (p0) REVERT: G 75 LEU cc_start: 0.9301 (mt) cc_final: 0.8826 (mt) REVERT: G 76 PHE cc_start: 0.8298 (m-10) cc_final: 0.7698 (m-10) REVERT: G 108 LEU cc_start: 0.9345 (tp) cc_final: 0.9087 (tp) REVERT: C 95 MET cc_start: 0.9155 (ppp) cc_final: 0.8727 (ppp) REVERT: C 104 MET cc_start: 0.9205 (mmt) cc_final: 0.8989 (mmt) REVERT: C 373 MET cc_start: 0.8610 (mtp) cc_final: 0.8252 (tpp) REVERT: E 619 LEU cc_start: 0.9091 (tp) cc_final: 0.8887 (tp) REVERT: E 630 GLU cc_start: 0.8678 (pt0) cc_final: 0.8253 (pt0) REVERT: I 13 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8508 (mmmm) REVERT: I 46 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8087 (mm-30) REVERT: I 72 ASP cc_start: 0.8317 (t70) cc_final: 0.8046 (t0) REVERT: I 108 LEU cc_start: 0.9096 (tp) cc_final: 0.8782 (tp) REVERT: D 69 TRP cc_start: 0.7863 (m-90) cc_final: 0.7419 (m-90) REVERT: D 95 MET cc_start: 0.9071 (ppp) cc_final: 0.8842 (ppp) REVERT: D 308 HIS cc_start: 0.8196 (m90) cc_final: 0.7640 (m90) REVERT: D 373 MET cc_start: 0.8706 (mtp) cc_final: 0.8066 (mmm) REVERT: F 628 TRP cc_start: 0.8613 (m100) cc_final: 0.7732 (m100) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.3175 time to fit residues: 165.7593 Evaluate side-chains 245 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100BGLN ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN C 413 HIS ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN F 590 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 19959 Z= 0.402 Angle : 0.840 11.734 27072 Z= 0.429 Chirality : 0.052 0.370 3237 Planarity : 0.006 0.070 3336 Dihedral : 8.514 57.122 4098 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.16 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.71 (0.17), residues: 2280 helix: 0.21 (0.25), residues: 405 sheet: 0.24 (0.20), residues: 621 loop : -1.06 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP E 628 HIS 0.007 0.002 HIS H 79 PHE 0.030 0.003 PHE D 53 TYR 0.022 0.003 TYR F 638 ARG 0.007 0.001 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8345 (mmmm) REVERT: H 27 ASP cc_start: 0.9089 (p0) cc_final: 0.8887 (p0) REVERT: H 72 ASP cc_start: 0.7919 (t0) cc_final: 0.7540 (t0) REVERT: H 75 LEU cc_start: 0.8952 (mt) cc_final: 0.8406 (mt) REVERT: H 100 TYR cc_start: 0.5796 (m-80) cc_final: 0.5280 (m-80) REVERT: H 108 LEU cc_start: 0.9169 (tp) cc_final: 0.8857 (tp) REVERT: L 96 GLU cc_start: 0.8789 (pm20) cc_final: 0.8187 (pm20) REVERT: L 97 PHE cc_start: 0.8696 (m-80) cc_final: 0.7867 (m-10) REVERT: A 95 MET cc_start: 0.9235 (ppp) cc_final: 0.8280 (ppp) REVERT: A 308 HIS cc_start: 0.8502 (m90) cc_final: 0.7911 (m90) REVERT: A 373 MET cc_start: 0.8845 (mtp) cc_final: 0.8457 (mmm) REVERT: A 475 MET cc_start: 0.8707 (mmm) cc_final: 0.8433 (mmm) REVERT: B 584 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8620 (tm-30) REVERT: B 588 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8684 (tpp80) REVERT: B 655 LYS cc_start: 0.9142 (pttm) cc_final: 0.8778 (pttm) REVERT: G 4 LEU cc_start: 0.8777 (mt) cc_final: 0.8515 (mt) REVERT: G 27 ASP cc_start: 0.9201 (p0) cc_final: 0.8794 (p0) REVERT: G 31 ARG cc_start: 0.8980 (mtt-85) cc_final: 0.8737 (tpp80) REVERT: G 36 TRP cc_start: 0.8977 (m100) cc_final: 0.8509 (m-10) REVERT: G 46 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8009 (mm-30) REVERT: G 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7998 (t0) REVERT: G 74 ASP cc_start: 0.8652 (p0) cc_final: 0.8429 (p0) REVERT: G 75 LEU cc_start: 0.9313 (mt) cc_final: 0.8876 (mt) REVERT: G 76 PHE cc_start: 0.8447 (m-10) cc_final: 0.7846 (m-10) REVERT: G 108 LEU cc_start: 0.9454 (tp) cc_final: 0.9156 (tp) REVERT: J 97 PHE cc_start: 0.8821 (m-80) cc_final: 0.8596 (m-80) REVERT: C 95 MET cc_start: 0.9225 (ppp) cc_final: 0.8591 (ppp) REVERT: C 373 MET cc_start: 0.8516 (mtp) cc_final: 0.8093 (tpp) REVERT: E 575 GLN cc_start: 0.8765 (pp30) cc_final: 0.8503 (pp30) REVERT: I 13 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8498 (mmmm) REVERT: I 28 ILE cc_start: 0.8978 (mt) cc_final: 0.8078 (mt) REVERT: I 46 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8048 (mm-30) REVERT: I 60 SER cc_start: 0.9366 (t) cc_final: 0.9160 (p) REVERT: I 72 ASP cc_start: 0.8405 (t70) cc_final: 0.8129 (t0) REVERT: I 100 TYR cc_start: 0.6695 (m-10) cc_final: 0.6176 (m-10) REVERT: I 108 LEU cc_start: 0.9100 (tp) cc_final: 0.8752 (tp) REVERT: D 69 TRP cc_start: 0.7928 (m-90) cc_final: 0.7475 (m-90) REVERT: D 95 MET cc_start: 0.9187 (ppp) cc_final: 0.8861 (ppp) REVERT: D 195 ASN cc_start: 0.8722 (m110) cc_final: 0.8488 (m-40) REVERT: D 308 HIS cc_start: 0.8204 (m90) cc_final: 0.7546 (m90) REVERT: D 373 MET cc_start: 0.8746 (mtp) cc_final: 0.8266 (mmm) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3141 time to fit residues: 141.4015 Evaluate side-chains 226 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 GLN ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19959 Z= 0.285 Angle : 0.757 12.811 27072 Z= 0.388 Chirality : 0.051 0.376 3237 Planarity : 0.005 0.072 3336 Dihedral : 8.341 59.763 4098 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.37 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.17), residues: 2280 helix: 0.26 (0.25), residues: 405 sheet: 0.37 (0.20), residues: 609 loop : -1.03 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 427 HIS 0.004 0.001 HIS D 105 PHE 0.024 0.003 PHE I 97 TYR 0.021 0.002 TYR G 100E ARG 0.013 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8324 (mmmm) REVERT: H 46 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8334 (mm-30) REVERT: H 72 ASP cc_start: 0.8122 (t0) cc_final: 0.7699 (t0) REVERT: H 75 LEU cc_start: 0.8933 (mt) cc_final: 0.8336 (mt) REVERT: H 100 TYR cc_start: 0.5559 (m-80) cc_final: 0.5101 (m-80) REVERT: H 108 LEU cc_start: 0.9193 (tp) cc_final: 0.8888 (tp) REVERT: L 96 GLU cc_start: 0.8772 (pm20) cc_final: 0.8170 (pm20) REVERT: L 97 PHE cc_start: 0.8621 (m-80) cc_final: 0.7807 (m-10) REVERT: A 95 MET cc_start: 0.9176 (ppp) cc_final: 0.8312 (ppp) REVERT: A 308 HIS cc_start: 0.8470 (m90) cc_final: 0.7841 (m90) REVERT: A 373 MET cc_start: 0.8729 (mtp) cc_final: 0.8042 (tpp) REVERT: A 475 MET cc_start: 0.8575 (mmm) cc_final: 0.8343 (mmm) REVERT: B 575 GLN cc_start: 0.8917 (pp30) cc_final: 0.8528 (pp30) REVERT: B 584 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 588 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8111 (ttm-80) REVERT: B 596 TRP cc_start: 0.8742 (m-10) cc_final: 0.8521 (m-90) REVERT: B 630 GLU cc_start: 0.8700 (pt0) cc_final: 0.8456 (pt0) REVERT: B 655 LYS cc_start: 0.9055 (pttm) cc_final: 0.8662 (pttm) REVERT: G 27 ASP cc_start: 0.9123 (p0) cc_final: 0.8546 (p0) REVERT: G 28 ILE cc_start: 0.9334 (mm) cc_final: 0.8856 (mm) REVERT: G 36 TRP cc_start: 0.8960 (m100) cc_final: 0.8370 (m-10) REVERT: G 46 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8005 (mm-30) REVERT: G 74 ASP cc_start: 0.8657 (p0) cc_final: 0.8390 (p0) REVERT: G 75 LEU cc_start: 0.9305 (mt) cc_final: 0.8827 (mt) REVERT: G 76 PHE cc_start: 0.8426 (m-10) cc_final: 0.7994 (m-10) REVERT: G 108 LEU cc_start: 0.9416 (tp) cc_final: 0.9143 (tp) REVERT: C 95 MET cc_start: 0.9142 (ppp) cc_final: 0.8567 (ppp) REVERT: C 373 MET cc_start: 0.8550 (mtp) cc_final: 0.8228 (tpp) REVERT: E 584 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8676 (tm-30) REVERT: E 588 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8480 (tpp80) REVERT: E 626 MET cc_start: 0.7726 (mmm) cc_final: 0.7005 (tpt) REVERT: I 13 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8478 (mmmm) REVERT: I 46 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8111 (mm-30) REVERT: I 60 SER cc_start: 0.9379 (t) cc_final: 0.9100 (m) REVERT: I 72 ASP cc_start: 0.8181 (t70) cc_final: 0.7905 (t0) REVERT: I 108 LEU cc_start: 0.9119 (tp) cc_final: 0.8775 (tp) REVERT: K 97 PHE cc_start: 0.8672 (m-80) cc_final: 0.8401 (m-80) REVERT: D 69 TRP cc_start: 0.7877 (m-90) cc_final: 0.7467 (m-90) REVERT: D 95 MET cc_start: 0.9139 (ppp) cc_final: 0.8734 (ppp) REVERT: D 195 ASN cc_start: 0.8627 (m110) cc_final: 0.8406 (m110) REVERT: D 308 HIS cc_start: 0.8284 (m90) cc_final: 0.7560 (m90) REVERT: D 316 TRP cc_start: 0.7716 (m-90) cc_final: 0.7475 (m-90) REVERT: D 373 MET cc_start: 0.8725 (mtp) cc_final: 0.8260 (mmm) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.3279 time to fit residues: 150.5699 Evaluate side-chains 227 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19959 Z= 0.208 Angle : 0.723 12.319 27072 Z= 0.367 Chirality : 0.050 0.372 3237 Planarity : 0.004 0.070 3336 Dihedral : 7.942 58.060 4098 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.40 (0.17), residues: 2280 helix: 0.47 (0.25), residues: 408 sheet: 0.47 (0.20), residues: 636 loop : -0.91 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 427 HIS 0.005 0.001 HIS I 79 PHE 0.032 0.002 PHE G 76 TYR 0.020 0.001 TYR E 638 ARG 0.009 0.000 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8081 (t0) cc_final: 0.7633 (t0) REVERT: H 75 LEU cc_start: 0.8891 (mt) cc_final: 0.8309 (mt) REVERT: H 100 TYR cc_start: 0.5289 (m-80) cc_final: 0.4997 (m-80) REVERT: H 108 LEU cc_start: 0.9242 (tp) cc_final: 0.8890 (tp) REVERT: L 4 LEU cc_start: 0.8753 (tp) cc_final: 0.8332 (tp) REVERT: L 96 GLU cc_start: 0.8755 (pm20) cc_final: 0.8119 (pm20) REVERT: L 97 PHE cc_start: 0.8601 (m-80) cc_final: 0.7767 (m-10) REVERT: A 95 MET cc_start: 0.9175 (ppp) cc_final: 0.8416 (ppp) REVERT: A 308 HIS cc_start: 0.8444 (m90) cc_final: 0.7811 (m90) REVERT: A 373 MET cc_start: 0.8703 (mtp) cc_final: 0.8043 (tpp) REVERT: A 475 MET cc_start: 0.8509 (mmm) cc_final: 0.8299 (mmm) REVERT: B 584 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 596 TRP cc_start: 0.8509 (m-10) cc_final: 0.8262 (m-90) REVERT: B 630 GLU cc_start: 0.8675 (pt0) cc_final: 0.8369 (pt0) REVERT: B 655 LYS cc_start: 0.8926 (pttm) cc_final: 0.8545 (pttm) REVERT: G 27 ASP cc_start: 0.8892 (p0) cc_final: 0.8692 (p0) REVERT: G 31 ARG cc_start: 0.8908 (mtt90) cc_final: 0.8701 (tpp80) REVERT: G 36 TRP cc_start: 0.8939 (m100) cc_final: 0.8367 (m-10) REVERT: G 46 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7963 (mm-30) REVERT: G 72 ASP cc_start: 0.8117 (t0) cc_final: 0.7720 (t0) REVERT: G 74 ASP cc_start: 0.8580 (p0) cc_final: 0.8204 (p0) REVERT: G 75 LEU cc_start: 0.9177 (mt) cc_final: 0.8609 (mt) REVERT: G 108 LEU cc_start: 0.9338 (tp) cc_final: 0.9112 (tp) REVERT: J 33 MET cc_start: 0.7885 (pmm) cc_final: 0.7565 (pmm) REVERT: J 78 MET cc_start: 0.7081 (mtp) cc_final: 0.6333 (ttm) REVERT: C 95 MET cc_start: 0.9122 (ppp) cc_final: 0.8583 (ppp) REVERT: C 308 HIS cc_start: 0.8245 (m90) cc_final: 0.7645 (m90) REVERT: C 373 MET cc_start: 0.8507 (mtp) cc_final: 0.8161 (tpp) REVERT: E 535 MET cc_start: 0.7720 (tpp) cc_final: 0.7398 (tpp) REVERT: E 584 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8609 (tm-30) REVERT: E 588 ARG cc_start: 0.8830 (tpp80) cc_final: 0.8431 (tpp80) REVERT: E 596 TRP cc_start: 0.8764 (m-10) cc_final: 0.8383 (m-90) REVERT: E 619 LEU cc_start: 0.9022 (tp) cc_final: 0.8814 (tp) REVERT: I 13 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8452 (mmmm) REVERT: I 31 ARG cc_start: 0.9008 (ttm170) cc_final: 0.8806 (tpm170) REVERT: I 46 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8012 (mm-30) REVERT: I 60 SER cc_start: 0.9316 (t) cc_final: 0.9046 (m) REVERT: I 72 ASP cc_start: 0.8240 (t70) cc_final: 0.7972 (t0) REVERT: I 81 ASP cc_start: 0.6834 (p0) cc_final: 0.6549 (p0) REVERT: I 108 LEU cc_start: 0.9113 (tp) cc_final: 0.8831 (tp) REVERT: K 71 TYR cc_start: 0.5822 (t80) cc_final: 0.5106 (t80) REVERT: D 95 MET cc_start: 0.9074 (ppp) cc_final: 0.8782 (ppp) REVERT: D 195 ASN cc_start: 0.8447 (m110) cc_final: 0.8155 (m110) REVERT: D 308 HIS cc_start: 0.8247 (m90) cc_final: 0.7516 (m90) REVERT: D 373 MET cc_start: 0.8652 (mtp) cc_final: 0.8247 (ttm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3123 time to fit residues: 151.6094 Evaluate side-chains 233 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 209 optimal weight: 0.4980 chunk 180 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN B 543 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 HIS F 543 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 19959 Z= 0.358 Angle : 0.808 10.995 27072 Z= 0.412 Chirality : 0.051 0.393 3237 Planarity : 0.005 0.071 3336 Dihedral : 8.159 56.243 4098 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.33 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.17), residues: 2280 helix: 0.21 (0.25), residues: 408 sheet: 0.42 (0.21), residues: 570 loop : -1.00 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP I 36 HIS 0.005 0.002 HIS C 105 PHE 0.025 0.003 PHE G 76 TYR 0.020 0.002 TYR E 638 ARG 0.015 0.001 ARG J 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8313 (mmmm) REVERT: H 72 ASP cc_start: 0.8168 (t0) cc_final: 0.7671 (t0) REVERT: H 75 LEU cc_start: 0.8957 (mt) cc_final: 0.8369 (mt) REVERT: H 100 TYR cc_start: 0.5749 (m-80) cc_final: 0.5309 (m-80) REVERT: H 108 LEU cc_start: 0.9224 (tp) cc_final: 0.8906 (tp) REVERT: L 96 GLU cc_start: 0.8656 (pm20) cc_final: 0.8090 (pm20) REVERT: L 97 PHE cc_start: 0.8683 (m-80) cc_final: 0.7901 (m-10) REVERT: A 95 MET cc_start: 0.9223 (ppp) cc_final: 0.8090 (ppp) REVERT: A 308 HIS cc_start: 0.8516 (m90) cc_final: 0.7926 (m90) REVERT: A 373 MET cc_start: 0.8720 (mtp) cc_final: 0.8507 (mmm) REVERT: A 475 MET cc_start: 0.8605 (mmm) cc_final: 0.8379 (mmp) REVERT: B 588 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8238 (ttm170) REVERT: B 655 LYS cc_start: 0.9021 (pttm) cc_final: 0.8617 (pttm) REVERT: G 4 LEU cc_start: 0.8693 (mt) cc_final: 0.8388 (mt) REVERT: G 46 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7955 (mm-30) REVERT: G 72 ASP cc_start: 0.8240 (t0) cc_final: 0.7927 (t0) REVERT: G 74 ASP cc_start: 0.8116 (p0) cc_final: 0.7669 (p0) REVERT: G 75 LEU cc_start: 0.9096 (mt) cc_final: 0.8528 (mt) REVERT: G 108 LEU cc_start: 0.9397 (tp) cc_final: 0.9123 (tp) REVERT: J 78 MET cc_start: 0.7215 (mtp) cc_final: 0.6517 (ttm) REVERT: J 97 PHE cc_start: 0.8672 (m-80) cc_final: 0.8443 (m-80) REVERT: C 68 VAL cc_start: 0.8623 (t) cc_final: 0.8306 (t) REVERT: C 95 MET cc_start: 0.9220 (ppp) cc_final: 0.8428 (ppp) REVERT: C 373 MET cc_start: 0.8581 (mtp) cc_final: 0.8178 (tpp) REVERT: E 535 MET cc_start: 0.8063 (tpp) cc_final: 0.7560 (tpp) REVERT: E 584 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8629 (tm-30) REVERT: E 588 ARG cc_start: 0.8835 (tpp80) cc_final: 0.8426 (tpp80) REVERT: E 619 LEU cc_start: 0.9023 (tp) cc_final: 0.8785 (tp) REVERT: E 630 GLU cc_start: 0.8787 (pt0) cc_final: 0.8535 (pt0) REVERT: I 13 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8517 (mmmm) REVERT: I 46 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7951 (mm-30) REVERT: I 72 ASP cc_start: 0.8233 (t70) cc_final: 0.7942 (t0) REVERT: I 81 ASP cc_start: 0.6955 (p0) cc_final: 0.6612 (p0) REVERT: I 108 LEU cc_start: 0.9180 (tp) cc_final: 0.8848 (tp) REVERT: K 78 MET cc_start: 0.6616 (ptp) cc_final: 0.6257 (ptm) REVERT: K 97 PHE cc_start: 0.8721 (m-80) cc_final: 0.8506 (m-80) REVERT: D 95 MET cc_start: 0.9204 (ppp) cc_final: 0.8907 (ppp) REVERT: D 308 HIS cc_start: 0.8356 (m90) cc_final: 0.7609 (m90) REVERT: D 316 TRP cc_start: 0.7883 (m-90) cc_final: 0.7679 (m-90) REVERT: D 373 MET cc_start: 0.8759 (mtp) cc_final: 0.8300 (mmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3298 time to fit residues: 144.0690 Evaluate side-chains 215 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 186 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN I 3 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.070871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056226 restraints weight = 86797.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058165 restraints weight = 50653.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059519 restraints weight = 34899.267| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19959 Z= 0.231 Angle : 0.744 11.485 27072 Z= 0.378 Chirality : 0.051 0.362 3237 Planarity : 0.005 0.069 3336 Dihedral : 7.925 55.973 4098 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.15 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.51 (0.17), residues: 2280 helix: 0.28 (0.25), residues: 411 sheet: 0.52 (0.20), residues: 597 loop : -0.98 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP B 596 HIS 0.006 0.001 HIS I 79 PHE 0.053 0.002 PHE I 76 TYR 0.020 0.002 TYR E 638 ARG 0.007 0.000 ARG J 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.92 seconds wall clock time: 77 minutes 5.82 seconds (4625.82 seconds total)