Starting phenix.real_space_refine on Mon Mar 18 01:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo0_21256/03_2024/6vo0_21256.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo0_21256/03_2024/6vo0_21256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo0_21256/03_2024/6vo0_21256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo0_21256/03_2024/6vo0_21256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo0_21256/03_2024/6vo0_21256.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo0_21256/03_2024/6vo0_21256.pdb" } resolution = 3.52 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= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12225 2.51 5 N 3267 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "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 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "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 "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "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 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "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 "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 318": "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 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 468": "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: 19494 Number of models: 1 Model: "" Number of chains: 36 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "G" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "C" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 10.55, per 1000 atoms: 0.54 Number of scatterers: 19494 At special positions: 0 Unit cell: (165.83, 162.74, 146.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3870 8.00 N 3267 7.00 C 12225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35A" - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.10 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35A" - pdb=" SG CYS I 50 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.10 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 608 " - " ASN A 276 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 392 " " NAG A 617 " - " ASN A 363 " " NAG A 618 " - " ASN A 234 " " NAG A 619 " - " ASN A 197 " " NAG A 624 " - " ASN A 88 " " NAG C 608 " - " ASN C 276 " " NAG C 611 " - " ASN C 301 " " NAG C 612 " - " ASN C 332 " " NAG C 613 " - " ASN C 386 " " NAG C 614 " - " ASN C 392 " " NAG C 617 " - " ASN C 363 " " NAG C 618 " - " ASN C 234 " " NAG C 619 " - " ASN C 197 " " NAG C 624 " - " ASN C 88 " " NAG D 608 " - " ASN D 276 " " NAG D 611 " - " ASN D 301 " " NAG D 612 " - " ASN D 332 " " NAG D 613 " - " ASN D 386 " " NAG D 614 " - " ASN D 392 " " NAG D 617 " - " ASN D 363 " " NAG D 618 " - " ASN D 234 " " NAG D 619 " - " ASN D 197 " " NAG D 624 " - " ASN D 88 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 137 " " NAG T 1 " - " ASN C 133 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 295 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 137 " " NAG a 1 " - " ASN D 133 " " NAG b 1 " - " ASN D 160 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 295 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 137 " Time building additional restraints: 8.43 Conformation dependent library (CDL) restraints added in 3.4 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.1% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.661A 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 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.229A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.780A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.661A 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 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.229A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.745A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 639 through 662 removed outlier: 4.781A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'D' and resid 98 through 115 removed outlier: 3.661A 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 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 476 through 481 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.228A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 662 removed outlier: 4.780A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.675A pdb=" N GLY L 100 " --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER H 96 " --> pdb=" O VAL H 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL H 100H" --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL A 242 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS A 85 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 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 129 through 130 Processing sheet with id=AB2, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AB4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.459A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 14 removed outlier: 4.674A pdb=" N GLY J 100 " --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER G 96 " --> pdb=" O VAL G 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL G 100H" --> pdb=" O SER G 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL C 242 " --> pdb=" O HIS C 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS C 85 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AD1, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AD2, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.459A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (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 14 removed outlier: 4.675A pdb=" N GLY K 100 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER I 96 " --> pdb=" O VAL I 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL I 100H" --> pdb=" O SER I 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AE3, first strand: chain 'D' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL D 242 " --> pdb=" O HIS D 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS D 85 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE5, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE6, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AE7, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AE8, first strand: chain 'D' and resid 158 through 162 Processing sheet with id=AE9, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.117A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.460A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4876 1.32 - 1.46: 6261 1.46 - 1.60: 8579 1.60 - 1.73: 15 1.73 - 1.87: 159 Bond restraints: 19890 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG e 2 " pdb=" O5 NAG e 2 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 19885 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.68: 376 104.68 - 112.05: 9507 112.05 - 119.42: 7544 119.42 - 126.79: 9301 126.79 - 134.16: 281 Bond angle restraints: 27009 Sorted by residual: angle pdb=" N SER J 90 " pdb=" CA SER J 90 " pdb=" C SER J 90 " ideal model delta sigma weight residual 111.07 121.28 -10.21 1.07e+00 8.73e-01 9.11e+01 angle pdb=" N SER K 90 " pdb=" CA SER K 90 " pdb=" C SER K 90 " ideal model delta sigma weight residual 111.07 121.27 -10.20 1.07e+00 8.73e-01 9.09e+01 angle pdb=" N SER L 90 " pdb=" CA SER L 90 " pdb=" C SER L 90 " ideal model delta sigma weight residual 111.07 121.25 -10.18 1.07e+00 8.73e-01 9.04e+01 angle pdb=" C ILE I 48 " pdb=" CA ILE I 48 " pdb=" CB ILE I 48 " ideal model delta sigma weight residual 111.71 104.26 7.45 8.50e-01 1.38e+00 7.67e+01 angle pdb=" C ILE G 48 " pdb=" CA ILE G 48 " pdb=" CB ILE G 48 " ideal model delta sigma weight residual 111.71 104.27 7.44 8.50e-01 1.38e+00 7.65e+01 ... (remaining 27004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 12321 21.52 - 43.04: 363 43.04 - 64.55: 99 64.55 - 86.07: 30 86.07 - 107.59: 12 Dihedral angle restraints: 12825 sinusoidal: 6039 harmonic: 6786 Sorted by residual: dihedral pdb=" O4 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C5 BMA c 3 " pdb=" O5 BMA c 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.88 107.59 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.84 107.55 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C5 BMA V 3 " pdb=" O5 BMA V 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.83 107.54 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 12822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2230 0.098 - 0.195: 810 0.195 - 0.293: 182 0.293 - 0.390: 18 0.390 - 0.488: 3 Chirality restraints: 3243 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.81e+01 ... (remaining 3240 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 109 " 0.047 2.00e-02 2.50e+03 9.68e-02 9.37e+01 pdb=" C VAL H 109 " -0.167 2.00e-02 2.50e+03 pdb=" O VAL H 109 " 0.062 2.00e-02 2.50e+03 pdb=" OXT VAL H 109 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 109 " -0.047 2.00e-02 2.50e+03 9.67e-02 9.36e+01 pdb=" C VAL G 109 " 0.167 2.00e-02 2.50e+03 pdb=" O VAL G 109 " -0.062 2.00e-02 2.50e+03 pdb=" OXT VAL G 109 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 109 " 0.047 2.00e-02 2.50e+03 9.67e-02 9.35e+01 pdb=" C VAL I 109 " -0.167 2.00e-02 2.50e+03 pdb=" O VAL I 109 " 0.062 2.00e-02 2.50e+03 pdb=" OXT VAL I 109 " 0.058 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8036 2.88 - 3.39: 17290 3.39 - 3.89: 33084 3.89 - 4.40: 37992 4.40 - 4.90: 61141 Nonbonded interactions: 157543 Sorted by model distance: nonbonded pdb=" OG1 THR H 72 " pdb=" OG1 THR H 76 " model vdw 2.380 2.440 nonbonded pdb=" OG1 THR I 72 " pdb=" OG1 THR I 76 " model vdw 2.380 2.440 nonbonded pdb=" OG1 THR G 72 " pdb=" OG1 THR G 76 " model vdw 2.380 2.440 nonbonded pdb=" OD2 ASP A 57 " pdb=" NZ LYS A 59 " model vdw 2.404 2.520 nonbonded pdb=" OD2 ASP D 57 " pdb=" NZ LYS D 59 " model vdw 2.405 2.520 ... (remaining 157538 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 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.670 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 55.270 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.310 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.022 0.147 19890 Z= 1.412 Angle : 1.796 12.713 27009 Z= 1.182 Chirality : 0.104 0.488 3243 Planarity : 0.010 0.097 3339 Dihedral : 11.748 107.590 8331 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.64 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 0.22 (0.17), residues: 2310 helix: -0.48 (0.23), residues: 447 sheet: 0.49 (0.18), residues: 708 loop : 0.36 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.010 TRP J 35 HIS 0.013 0.003 HIS H 100F PHE 0.027 0.005 PHE A 53 TYR 0.067 0.008 TYR B 638 ARG 0.009 0.001 ARG K 95C *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 2.348 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: L 62 PHE cc_start: 0.8541 (m-80) cc_final: 0.8228 (m-80) REVERT: H 82 LEU cc_start: 0.8814 (mt) cc_final: 0.8563 (mp) REVERT: A 481 SER cc_start: 0.8662 (p) cc_final: 0.8400 (t) REVERT: B 543 ASN cc_start: 0.8300 (t0) cc_final: 0.8087 (t0) REVERT: G 82 LEU cc_start: 0.8803 (mt) cc_final: 0.8548 (mp) REVERT: C 481 SER cc_start: 0.8745 (p) cc_final: 0.8510 (t) REVERT: E 658 GLN cc_start: 0.7587 (tt0) cc_final: 0.7349 (tm-30) REVERT: K 39 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8189 (mmmm) REVERT: K 73 LEU cc_start: 0.8841 (mt) cc_final: 0.8533 (tp) REVERT: D 180 ASP cc_start: 0.7790 (m-30) cc_final: 0.7527 (m-30) REVERT: D 481 SER cc_start: 0.8680 (p) cc_final: 0.8445 (t) REVERT: F 543 ASN cc_start: 0.8246 (t0) cc_final: 0.7995 (t0) REVERT: F 658 GLN cc_start: 0.7644 (tt0) cc_final: 0.7331 (tm-30) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.3378 time to fit residues: 267.6578 Evaluate side-chains 266 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 100FHIS A 72 HIS A 195 ASN A 216 HIS A 374 HIS A 478 ASN B 625 ASN B 653 GLN J 38 GLN J 89 GLN J 91 ASN C 72 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 216 HIS C 300 ASN E 625 ASN E 653 GLN K 38 GLN K 91 ASN I 39 GLN I 100FHIS D 72 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 352 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19890 Z= 0.282 Angle : 0.779 9.808 27009 Z= 0.412 Chirality : 0.048 0.225 3243 Planarity : 0.005 0.049 3339 Dihedral : 8.687 60.292 4035 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 2.87 % Allowed : 9.39 % Favored : 87.74 % 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: -0.16 (0.17), residues: 2310 helix: 0.70 (0.26), residues: 417 sheet: 0.20 (0.18), residues: 708 loop : -0.51 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 614 HIS 0.009 0.001 HIS I 100F PHE 0.017 0.002 PHE L 92 TYR 0.024 0.002 TYR H 100C ARG 0.006 0.001 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 350 time to evaluate : 2.129 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: L 24 GLN cc_start: 0.8461 (tp40) cc_final: 0.8242 (tp40) REVERT: L 104 VAL cc_start: 0.9071 (t) cc_final: 0.8835 (t) REVERT: L 107 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7089 (tptt) REVERT: H 53 ASP cc_start: 0.8654 (m-30) cc_final: 0.8336 (t0) REVERT: A 180 ASP cc_start: 0.7853 (m-30) cc_final: 0.7417 (m-30) REVERT: A 481 SER cc_start: 0.8605 (p) cc_final: 0.8404 (t) REVERT: B 543 ASN cc_start: 0.8269 (t0) cc_final: 0.8053 (t0) REVERT: J 4 MET cc_start: 0.6682 (mtp) cc_final: 0.6471 (mtm) REVERT: G 23 LYS cc_start: 0.8818 (tptm) cc_final: 0.8596 (tttp) REVERT: G 38 ARG cc_start: 0.8124 (ptt180) cc_final: 0.7814 (ptt180) REVERT: G 86 ASP cc_start: 0.8296 (m-30) cc_final: 0.7786 (m-30) REVERT: C 150 MET cc_start: 0.8530 (tpp) cc_final: 0.8279 (tpp) REVERT: I 100 TYR cc_start: 0.8430 (t80) cc_final: 0.8215 (t80) REVERT: D 150 MET cc_start: 0.8654 (tpp) cc_final: 0.8403 (tpp) REVERT: D 180 ASP cc_start: 0.7839 (m-30) cc_final: 0.7523 (m-30) REVERT: D 481 SER cc_start: 0.8636 (p) cc_final: 0.8424 (t) REVERT: F 543 ASN cc_start: 0.8286 (t0) cc_final: 0.8055 (t0) REVERT: F 601 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7895 (ptmt) REVERT: F 659 ASP cc_start: 0.8713 (m-30) cc_final: 0.8423 (m-30) outliers start: 59 outliers final: 28 residues processed: 379 average time/residue: 0.2928 time to fit residues: 172.6834 Evaluate side-chains 294 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 264 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 612 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.0010 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 189 optimal weight: 0.4980 chunk 211 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 352 HIS B 625 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN G 39 GLN G 100FHIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19890 Z= 0.188 Angle : 0.651 9.041 27009 Z= 0.344 Chirality : 0.046 0.225 3243 Planarity : 0.004 0.052 3339 Dihedral : 6.834 39.455 4035 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.50 % Favored : 94.85 % Rotamer: Outliers : 2.68 % Allowed : 11.44 % Favored : 85.89 % 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: -0.18 (0.17), residues: 2310 helix: 0.98 (0.26), residues: 417 sheet: 0.16 (0.18), residues: 726 loop : -0.65 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 96 HIS 0.005 0.001 HIS G 100F PHE 0.015 0.002 PHE G 98 TYR 0.024 0.002 TYR I 100C ARG 0.004 0.000 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 293 time to evaluate : 2.243 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: L 22 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7840 (tptt) REVERT: L 24 GLN cc_start: 0.8296 (tp40) cc_final: 0.7856 (tp40) REVERT: L 94 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7736 (tp) REVERT: H 4 LEU cc_start: 0.8842 (mm) cc_final: 0.8494 (mm) REVERT: A 180 ASP cc_start: 0.7780 (m-30) cc_final: 0.7441 (m-30) REVERT: J 4 MET cc_start: 0.7025 (mtp) cc_final: 0.6729 (mtm) REVERT: G 23 LYS cc_start: 0.8870 (tptm) cc_final: 0.8654 (tttp) REVERT: K 22 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (tptt) REVERT: K 24 GLN cc_start: 0.8140 (tp40) cc_final: 0.7795 (tp40) REVERT: K 38 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: I 4 LEU cc_start: 0.8847 (mm) cc_final: 0.8441 (mm) REVERT: D 180 ASP cc_start: 0.7733 (m-30) cc_final: 0.7454 (m-30) outliers start: 55 outliers final: 25 residues processed: 318 average time/residue: 0.3002 time to fit residues: 147.6133 Evaluate side-chains 278 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 249 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19890 Z= 0.257 Angle : 0.654 9.599 27009 Z= 0.340 Chirality : 0.046 0.248 3243 Planarity : 0.004 0.054 3339 Dihedral : 6.164 42.043 4035 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.94 % Favored : 94.24 % Rotamer: Outliers : 3.16 % Allowed : 12.26 % Favored : 84.57 % 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: -0.25 (0.17), residues: 2310 helix: 0.94 (0.26), residues: 417 sheet: 0.08 (0.18), residues: 738 loop : -0.69 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 628 HIS 0.003 0.001 HIS C 216 PHE 0.016 0.002 PHE G 98 TYR 0.023 0.002 TYR G 100C ARG 0.005 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 266 time to evaluate : 2.094 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: L 22 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7871 (tptt) REVERT: L 24 GLN cc_start: 0.8412 (tp40) cc_final: 0.8022 (tp-100) REVERT: L 107 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7230 (tptt) REVERT: H 53 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8415 (t0) REVERT: A 150 MET cc_start: 0.8225 (mmm) cc_final: 0.7945 (mmm) REVERT: A 180 ASP cc_start: 0.7778 (m-30) cc_final: 0.7485 (m-30) REVERT: A 234 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7422 (t0) REVERT: J 4 MET cc_start: 0.7117 (mtp) cc_final: 0.6742 (mtp) REVERT: J 38 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: G 4 LEU cc_start: 0.8836 (mm) cc_final: 0.8501 (mm) REVERT: G 23 LYS cc_start: 0.8946 (tptm) cc_final: 0.8741 (tttp) REVERT: C 150 MET cc_start: 0.8070 (tpp) cc_final: 0.7367 (mmt) REVERT: K 38 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: I 5 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8420 (m) REVERT: D 180 ASP cc_start: 0.7769 (m-30) cc_final: 0.7491 (m-30) REVERT: D 234 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7293 (t0) outliers start: 65 outliers final: 34 residues processed: 304 average time/residue: 0.3064 time to fit residues: 143.2846 Evaluate side-chains 286 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19890 Z= 0.341 Angle : 0.679 7.900 27009 Z= 0.354 Chirality : 0.046 0.261 3243 Planarity : 0.004 0.053 3339 Dihedral : 6.348 46.391 4035 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.89 % Favored : 94.33 % Rotamer: Outliers : 3.16 % Allowed : 13.19 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2310 helix: 0.96 (0.27), residues: 414 sheet: 0.03 (0.19), residues: 693 loop : -0.88 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 628 HIS 0.004 0.001 HIS C 216 PHE 0.016 0.002 PHE G 98 TYR 0.021 0.002 TYR E 586 ARG 0.004 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 252 time to evaluate : 2.254 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: L 24 GLN cc_start: 0.8441 (tp40) cc_final: 0.8184 (tp40) REVERT: L 107 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7009 (tptt) REVERT: H 53 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8463 (t0) REVERT: A 234 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7567 (t0) REVERT: A 271 MET cc_start: 0.8170 (tpp) cc_final: 0.7573 (tpp) REVERT: J 38 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: J 77 ASP cc_start: 0.8683 (t0) cc_final: 0.8438 (t0) REVERT: G 82 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8172 (tt) REVERT: K 4 MET cc_start: 0.7433 (mmm) cc_final: 0.7196 (mmm) REVERT: K 38 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: D 180 ASP cc_start: 0.7863 (m-30) cc_final: 0.7618 (m-30) REVERT: D 234 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7580 (t0) outliers start: 65 outliers final: 40 residues processed: 293 average time/residue: 0.2925 time to fit residues: 133.9582 Evaluate side-chains 281 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 42 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19890 Z= 0.268 Angle : 0.654 11.391 27009 Z= 0.339 Chirality : 0.045 0.262 3243 Planarity : 0.004 0.053 3339 Dihedral : 6.244 47.537 4035 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.32 % Favored : 93.90 % Rotamer: Outliers : 3.36 % Allowed : 13.97 % Favored : 82.68 % 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: -0.46 (0.17), residues: 2310 helix: 0.94 (0.27), residues: 420 sheet: 0.02 (0.19), residues: 693 loop : -0.93 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 628 HIS 0.003 0.001 HIS C 216 PHE 0.018 0.002 PHE L 98 TYR 0.025 0.002 TYR E 586 ARG 0.010 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 251 time to evaluate : 2.117 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: L 24 GLN cc_start: 0.8308 (tp40) cc_final: 0.8067 (tp-100) REVERT: L 107 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7153 (tptt) REVERT: H 53 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (t0) REVERT: H 86 ASP cc_start: 0.8241 (m-30) cc_final: 0.7956 (m-30) REVERT: A 234 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7701 (t0) REVERT: A 271 MET cc_start: 0.8227 (tpp) cc_final: 0.7680 (tpp) REVERT: J 38 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: G 81 LEU cc_start: 0.8908 (mp) cc_final: 0.8530 (tp) REVERT: K 38 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: K 77 ASP cc_start: 0.8764 (t0) cc_final: 0.8524 (t0) REVERT: D 180 ASP cc_start: 0.7831 (m-30) cc_final: 0.7604 (m-30) REVERT: D 234 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7669 (t0) REVERT: D 271 MET cc_start: 0.7989 (tpt) cc_final: 0.7690 (tpp) outliers start: 69 outliers final: 42 residues processed: 293 average time/residue: 0.2943 time to fit residues: 134.8930 Evaluate side-chains 282 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19890 Z= 0.403 Angle : 0.735 11.478 27009 Z= 0.380 Chirality : 0.048 0.279 3243 Planarity : 0.005 0.053 3339 Dihedral : 6.731 52.027 4035 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.88 % Favored : 92.55 % Rotamer: Outliers : 3.07 % Allowed : 14.65 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2310 helix: 0.97 (0.27), residues: 405 sheet: -0.06 (0.19), residues: 717 loop : -1.27 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 631 HIS 0.005 0.001 HIS A 216 PHE 0.019 0.002 PHE G 98 TYR 0.024 0.002 TYR E 586 ARG 0.010 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 236 time to evaluate : 2.214 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: L 24 GLN cc_start: 0.8339 (tp40) cc_final: 0.8106 (tp-100) REVERT: L 77 ASP cc_start: 0.8855 (t0) cc_final: 0.8534 (t0) REVERT: L 107 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7154 (tptt) REVERT: H 53 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8407 (t0) REVERT: H 86 ASP cc_start: 0.8255 (m-30) cc_final: 0.7957 (m-30) REVERT: A 234 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7889 (t0) REVERT: A 271 MET cc_start: 0.8198 (tpp) cc_final: 0.7652 (tpp) REVERT: J 38 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: J 103 GLU cc_start: 0.8566 (tp30) cc_final: 0.8329 (tp30) REVERT: C 271 MET cc_start: 0.8230 (tpp) cc_final: 0.7904 (tpp) REVERT: K 21 ILE cc_start: 0.9201 (mt) cc_final: 0.8948 (mm) REVERT: K 38 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: D 234 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 271 MET cc_start: 0.7960 (tpt) cc_final: 0.7704 (tpp) outliers start: 63 outliers final: 45 residues processed: 276 average time/residue: 0.2987 time to fit residues: 128.0881 Evaluate side-chains 273 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 222 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 143 optimal weight: 0.0070 chunk 153 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19890 Z= 0.209 Angle : 0.658 13.927 27009 Z= 0.340 Chirality : 0.045 0.256 3243 Planarity : 0.004 0.052 3339 Dihedral : 6.298 50.373 4035 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.50 % Favored : 93.77 % Rotamer: Outliers : 2.19 % Allowed : 16.01 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2310 helix: 0.96 (0.26), residues: 420 sheet: 0.05 (0.19), residues: 696 loop : -1.27 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 631 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.002 PHE L 98 TYR 0.024 0.001 TYR E 586 ARG 0.007 0.000 ARG I 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 252 time to evaluate : 2.236 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: L 24 GLN cc_start: 0.8237 (tp40) cc_final: 0.7993 (tp-100) REVERT: L 107 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7103 (tptt) REVERT: H 53 ASP cc_start: 0.8637 (m-30) cc_final: 0.8414 (t0) REVERT: H 86 ASP cc_start: 0.8206 (m-30) cc_final: 0.7954 (m-30) REVERT: A 234 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7877 (t0) REVERT: A 271 MET cc_start: 0.8111 (tpp) cc_final: 0.7532 (tpp) REVERT: J 38 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: G 81 LEU cc_start: 0.8751 (mp) cc_final: 0.8443 (tp) REVERT: C 104 MET cc_start: 0.9282 (tpp) cc_final: 0.9066 (tpp) REVERT: C 150 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7803 (mmm) REVERT: K 21 ILE cc_start: 0.9145 (mt) cc_final: 0.8918 (mm) REVERT: K 38 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: I 15 GLU cc_start: 0.7913 (tp30) cc_final: 0.7311 (tp30) REVERT: D 234 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7793 (t0) REVERT: D 271 MET cc_start: 0.7884 (tpt) cc_final: 0.7584 (tpp) outliers start: 45 outliers final: 34 residues processed: 279 average time/residue: 0.2985 time to fit residues: 128.7999 Evaluate side-chains 275 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN J 37 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19890 Z= 0.227 Angle : 0.660 11.432 27009 Z= 0.340 Chirality : 0.045 0.266 3243 Planarity : 0.004 0.053 3339 Dihedral : 6.123 48.734 4035 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.06 % Favored : 93.25 % Rotamer: Outliers : 2.38 % Allowed : 16.20 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2310 helix: 0.98 (0.26), residues: 423 sheet: 0.08 (0.19), residues: 705 loop : -1.27 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 631 HIS 0.003 0.001 HIS A 374 PHE 0.015 0.002 PHE G 98 TYR 0.025 0.001 TYR E 586 ARG 0.007 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 2.050 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: L 24 GLN cc_start: 0.8186 (tp40) cc_final: 0.7910 (tp-100) REVERT: L 107 LYS cc_start: 0.8123 (pttm) cc_final: 0.6988 (tptt) REVERT: H 15 GLU cc_start: 0.8197 (tp30) cc_final: 0.7921 (tp30) REVERT: H 86 ASP cc_start: 0.8231 (m-30) cc_final: 0.7956 (m-30) REVERT: A 271 MET cc_start: 0.8107 (tpp) cc_final: 0.7510 (tpp) REVERT: J 38 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: G 4 LEU cc_start: 0.8567 (mm) cc_final: 0.8301 (mm) REVERT: C 104 MET cc_start: 0.9264 (tpp) cc_final: 0.9010 (tpp) REVERT: C 150 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7536 (mmm) REVERT: K 38 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: I 15 GLU cc_start: 0.8017 (tp30) cc_final: 0.7420 (tp30) REVERT: D 234 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7877 (t0) REVERT: D 271 MET cc_start: 0.7897 (tpt) cc_final: 0.7583 (tpp) outliers start: 49 outliers final: 38 residues processed: 283 average time/residue: 0.2788 time to fit residues: 123.4331 Evaluate side-chains 278 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 105 optimal weight: 0.4980 chunk 154 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 143 optimal weight: 0.0000 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19890 Z= 0.176 Angle : 0.653 10.683 27009 Z= 0.337 Chirality : 0.045 0.251 3243 Planarity : 0.004 0.054 3339 Dihedral : 5.864 45.722 4035 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.50 % Favored : 93.72 % Rotamer: Outliers : 1.90 % Allowed : 17.27 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.58 (0.17), residues: 2310 helix: 1.07 (0.26), residues: 426 sheet: 0.23 (0.20), residues: 696 loop : -1.34 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP F 631 HIS 0.002 0.000 HIS A 374 PHE 0.014 0.001 PHE L 98 TYR 0.025 0.001 TYR E 586 ARG 0.008 0.000 ARG I 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 2.341 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: L 107 LYS cc_start: 0.8017 (pttm) cc_final: 0.6886 (tptt) REVERT: H 15 GLU cc_start: 0.8181 (tp30) cc_final: 0.7646 (tp30) REVERT: H 86 ASP cc_start: 0.8217 (m-30) cc_final: 0.7957 (m-30) REVERT: A 271 MET cc_start: 0.8014 (tpp) cc_final: 0.7664 (tpp) REVERT: B 654 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 657 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8165 (mp0) REVERT: J 38 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: C 104 MET cc_start: 0.9247 (tpp) cc_final: 0.9026 (tpp) REVERT: K 65 SER cc_start: 0.8505 (p) cc_final: 0.8137 (m) REVERT: D 234 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7855 (t0) outliers start: 39 outliers final: 32 residues processed: 270 average time/residue: 0.2931 time to fit residues: 123.8603 Evaluate side-chains 269 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 27 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.064924 restraints weight = 57647.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067519 restraints weight = 28040.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069196 restraints weight = 18495.551| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19890 Z= 0.194 Angle : 0.654 11.075 27009 Z= 0.334 Chirality : 0.045 0.256 3243 Planarity : 0.004 0.054 3339 Dihedral : 5.743 43.601 4035 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.10 % Favored : 93.12 % Rotamer: Outliers : 1.95 % Allowed : 17.37 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.57 (0.17), residues: 2310 helix: 1.19 (0.26), residues: 426 sheet: 0.19 (0.20), residues: 687 loop : -1.33 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 631 HIS 0.002 0.000 HIS A 374 PHE 0.013 0.001 PHE L 98 TYR 0.026 0.001 TYR E 586 ARG 0.009 0.000 ARG D 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3862.10 seconds wall clock time: 72 minutes 14.36 seconds (4334.36 seconds total)