Starting phenix.real_space_refine on Mon Jul 22 23:42:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpi_34193/07_2024/8gpi_34193.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpi_34193/07_2024/8gpi_34193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpi_34193/07_2024/8gpi_34193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpi_34193/07_2024/8gpi_34193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpi_34193/07_2024/8gpi_34193.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gpi_34193/07_2024/8gpi_34193.cif" } resolution = 3.0 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= 0.030 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 117 5.16 5 C 12666 2.51 5 N 3297 2.21 5 O 4185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X GLU 102": "OE1" <-> "OE2" Residue "X GLU 275": "OE1" <-> "OE2" Residue "X PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 102": "OE1" <-> "OE2" Residue "Y ASP 113": "OD1" <-> "OD2" Residue "Y GLU 164": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 211": "OD1" <-> "OD2" Residue "Y GLU 275": "OE1" <-> "OE2" Residue "Y ASP 321": "OD1" <-> "OD2" Residue "Y ASP 325": "OD1" <-> "OD2" Residue "Y GLU 466": "OE1" <-> "OE2" Residue "Y PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 482": "OE1" <-> "OE2" Residue "Z GLU 153": "OE1" <-> "OE2" Residue "Z GLU 164": "OE1" <-> "OE2" Residue "Z TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 267": "OE1" <-> "OE2" Residue "Z GLU 269": "OE1" <-> "OE2" Residue "Z GLU 337": "OE1" <-> "OE2" Residue "Z GLU 466": "OE1" <-> "OE2" Residue "Z GLU 482": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20265 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "S" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "T" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "X" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "Y" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "Z" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" 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: "k" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" 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: "Z" 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: 11.44, per 1000 atoms: 0.56 Number of scatterers: 20265 At special positions: 0 Unit cell: (150.52, 155.82, 126.14, 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 117 16.00 O 4185 8.00 N 3297 7.00 C 12666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 605 " - pdb=" SG CYS X 501 " distance=2.03 Simple disulfide: pdb=" SG CYS S 598 " - pdb=" SG CYS S 604 " distance=2.03 Simple disulfide: pdb=" SG CYS S 605 " - pdb=" SG CYS Y 501 " distance=2.03 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 Simple disulfide: pdb=" SG CYS T 605 " - pdb=" SG CYS Z 501 " distance=2.03 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 119 " - pdb=" SG CYS X 205 " distance=2.03 Simple disulfide: pdb=" SG CYS X 126 " - pdb=" SG CYS X 196 " distance=2.03 Simple disulfide: pdb=" SG CYS X 131 " - pdb=" SG CYS X 157 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.05 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 119 " - pdb=" SG CYS Y 205 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 126 " - pdb=" SG CYS Y 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 131 " - pdb=" SG CYS Y 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 218 " - pdb=" SG CYS Y 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 296 " - pdb=" SG CYS Y 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 126 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 131 " - pdb=" SG CYS Z 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 218 " - pdb=" SG CYS Z 247 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 228 " - pdb=" SG CYS Z 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 296 " - pdb=" SG CYS Z 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 378 " - pdb=" SG CYS Z 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 385 " - pdb=" SG CYS Z 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN K 10 " - " MAN K 11 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN b 10 " - " MAN b 11 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN k 8 " - " MAN k 9 " " MAN k 10 " - " MAN k 11 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA M 3 " - " MAN M 4 " " BMA b 3 " - " MAN b 4 " " MAN b 7 " - " MAN b 8 " " BMA c 3 " - " MAN c 4 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 8 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 10 " " BMA M 3 " - " MAN M 5 " " BMA b 3 " - " MAN b 7 " " MAN b 7 " - " MAN b 10 " " BMA c 3 " - " MAN c 5 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 10 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG B 1 " - " ASN R 637 " " NAG F 1 " - " ASN S 637 " " NAG G 1 " - " ASN T 637 " " NAG I 1 " - " ASN X 156 " " NAG J 1 " - " ASN X 197 " " NAG K 1 " - " ASN X 234 " " NAG M 1 " - " ASN X 262 " " NAG N 1 " - " ASN X 444 " " NAG O 1 " - " ASN X 386 " " NAG P 1 " - " ASN X 276 " " NAG Q 1 " - " ASN X 289 " " NAG R 701 " - " ASN R 611 " " NAG S 701 " - " ASN S 611 " " NAG T 701 " - " ASN T 611 " " NAG U 1 " - " ASN X 339 " " NAG V 1 " - " ASN X 130 " " NAG W 1 " - " ASN Y 156 " " NAG X 701 " - " ASN X 88 " " NAG X 702 " - " ASN X 135 " " NAG X 703 " - " ASN X 149 " " NAG X 704 " - " ASN X 160 " " NAG X 705 " - " ASN X 241 " " NAG X 706 " - " ASN X 448 " " NAG X 707 " - " ASN X 301 " " NAG X 708 " - " ASN X 334 " " NAG Y 701 " - " ASN Y 88 " " NAG Y 702 " - " ASN Y 135 " " NAG Y 703 " - " ASN Y 149 " " NAG Y 704 " - " ASN Y 160 " " NAG Y 705 " - " ASN Y 241 " " NAG Y 706 " - " ASN Y 301 " " NAG Y 707 " - " ASN Y 334 " " NAG Y 708 " - " ASN Y 339 " " NAG Y 709 " - " ASN Y 448 " " NAG Z 701 " - " ASN Z 88 " " NAG Z 702 " - " ASN Z 135 " " NAG Z 703 " - " ASN Z 149 " " NAG Z 704 " - " ASN Z 160 " " NAG Z 705 " - " ASN Z 241 " " NAG Z 706 " - " ASN Z 448 " " NAG Z 707 " - " ASN Z 301 " " NAG Z 708 " - " ASN Z 334 " " NAG Z 709 " - " ASN Z 356 " " NAG a 1 " - " ASN Y 197 " " NAG b 1 " - " ASN Y 234 " " NAG c 1 " - " ASN Y 262 " " NAG d 1 " - " ASN Y 276 " " NAG e 1 " - " ASN Y 289 " " NAG f 1 " - " ASN Y 386 " " NAG g 1 " - " ASN Y 444 " " NAG h 1 " - " ASN Y 130 " " NAG i 1 " - " ASN Z 156 " " NAG j 1 " - " ASN Z 197 " " NAG k 1 " - " ASN Z 234 " " NAG l 1 " - " ASN Z 262 " " NAG m 1 " - " ASN Z 276 " " NAG n 1 " - " ASN Z 289 " " NAG o 1 " - " ASN Z 339 " " NAG p 1 " - " ASN Z 386 " " NAG q 1 " - " ASN Z 444 " " NAG r 1 " - " ASN Z 130 " Time building additional restraints: 9.41 Conformation dependent library (CDL) restraints added in 3.2 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 38 sheets defined 19.1% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.978A pdb=" N THR A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.599A pdb=" N PHE C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.563A pdb=" N ARG D 63 " --> pdb=" O HIS D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.029A pdb=" N THR D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.584A pdb=" N PHE E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.079A pdb=" N THR H 93 " --> pdb=" O SER H 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 536 through 544 removed outlier: 4.308A pdb=" N GLN R 540 " --> pdb=" O THR R 536 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN R 543 " --> pdb=" O VAL R 539 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU R 544 " --> pdb=" O GLN R 540 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 596 removed outlier: 3.701A pdb=" N TRP R 596 " --> pdb=" O PHE R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 625 Processing helix chain 'R' and resid 627 through 635 Processing helix chain 'R' and resid 638 through 663 Processing helix chain 'S' and resid 529 through 534 Processing helix chain 'S' and resid 537 through 544 removed outlier: 3.562A pdb=" N ALA S 541 " --> pdb=" O LEU S 537 " (cutoff:3.500A) Processing helix chain 'S' and resid 572 through 596 removed outlier: 3.662A pdb=" N TRP S 596 " --> pdb=" O PHE S 592 " (cutoff:3.500A) Processing helix chain 'S' and resid 618 through 625 Processing helix chain 'S' and resid 627 through 635 Processing helix chain 'S' and resid 638 through 663 Processing helix chain 'T' and resid 529 through 534 Processing helix chain 'T' and resid 538 through 544 Processing helix chain 'T' and resid 572 through 596 removed outlier: 3.600A pdb=" N TRP T 596 " --> pdb=" O PHE T 592 " (cutoff:3.500A) Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 663 removed outlier: 3.588A pdb=" N ASP T 644 " --> pdb=" O ASN T 640 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 117 removed outlier: 4.287A pdb=" N GLU X 102 " --> pdb=" O ASN X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 126 removed outlier: 3.667A pdb=" N CYS X 126 " --> pdb=" O THR X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 198 Processing helix chain 'X' and resid 335 through 350 Processing helix chain 'X' and resid 476 through 481 removed outlier: 3.748A pdb=" N SER X 481 " --> pdb=" O ASP X 477 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 116 removed outlier: 4.471A pdb=" N GLU Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 126 removed outlier: 3.662A pdb=" N CYS Y 126 " --> pdb=" O THR Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 350 Processing helix chain 'Y' and resid 368 through 373 removed outlier: 3.567A pdb=" N THR Y 372 " --> pdb=" O ASP Y 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET Y 373 " --> pdb=" O LEU Y 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 368 through 373' Processing helix chain 'Y' and resid 476 through 484 removed outlier: 3.639A pdb=" N SER Y 481 " --> pdb=" O ASP Y 477 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU Y 482 " --> pdb=" O ASN Y 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 116 removed outlier: 4.378A pdb=" N GLU Z 102 " --> pdb=" O ASN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 123 through 126 removed outlier: 3.615A pdb=" N CYS Z 126 " --> pdb=" O THR Z 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 123 through 126' Processing helix chain 'Z' and resid 149 through 152 removed outlier: 4.367A pdb=" N ASP Z 152 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 149 through 152' Processing helix chain 'Z' and resid 195 through 198 Processing helix chain 'Z' and resid 335 through 350 Processing helix chain 'Z' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR Z 372 " --> pdb=" O ASP Z 368 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Z 373 " --> pdb=" O LEU Z 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 368 through 373' Processing helix chain 'Z' and resid 475 through 484 removed outlier: 3.685A pdb=" N TRP Z 479 " --> pdb=" O ILE Z 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Z 482 " --> pdb=" O ASN Z 478 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR Z 484 " --> pdb=" O ARG Z 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 9 through 10 current: chain 'A' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 55 through 58 current: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.639A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'D' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 10 current: chain 'D' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 55 through 58 current: chain 'D' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'D' and resid 111 through 112 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 9 through 10 current: chain 'E' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 53 through 54 current: chain 'E' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 10 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 55 through 58 current: chain 'H' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'H' and resid 111 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 33 through 38 removed outlier: 6.364A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'R' and resid 603 through 609 removed outlier: 5.111A pdb=" N VAL X 36 " --> pdb=" O THR R 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 603 through 609 removed outlier: 5.426A pdb=" N VAL Y 36 " --> pdb=" O THR S 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 603 through 609 removed outlier: 4.940A pdb=" N VAL Z 36 " --> pdb=" O THR T 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 45 through 47 removed outlier: 4.409A pdb=" N VAL X 242 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'X' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'X' and resid 201 through 203 removed outlier: 6.544A pdb=" N LYS X 202 " --> pdb=" O TYR X 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 259 through 261 current: chain 'X' and resid 284 through 298 removed outlier: 7.446A pdb=" N SER X 293 " --> pdb=" O ASN X 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN X 334 " --> pdb=" O SER X 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 330 through 334 current: chain 'X' and resid 381 through 385 removed outlier: 4.035A pdb=" N PHE X 382 " --> pdb=" O LYS X 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 413 through 421 current: chain 'X' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'X' and resid 302 through 312 removed outlier: 6.887A pdb=" N THR X 303 " --> pdb=" O GLY X 320A" (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN X 315 " --> pdb=" O ILE X 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 45 through 47 removed outlier: 4.609A pdb=" N VAL Y 242 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'Y' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'Y' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'Y' and resid 202 through 203 removed outlier: 6.474A pdb=" N LYS Y 202 " --> pdb=" O TYR Y 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 259 through 261 current: chain 'Y' and resid 284 through 298 removed outlier: 7.370A pdb=" N SER Y 293 " --> pdb=" O ASN Y 334 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN Y 334 " --> pdb=" O SER Y 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 329 through 334 current: chain 'Y' and resid 381 through 385 removed outlier: 4.274A pdb=" N PHE Y 382 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 413 through 421 current: chain 'Y' and resid 465 through 470 Processing sheet with id=AD5, first strand: chain 'Y' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'Z' and resid 45 through 47 removed outlier: 4.575A pdb=" N VAL Z 242 " --> pdb=" O LEU Z 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'Z' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'Z' and resid 120 through 121 removed outlier: 3.927A pdb=" N VAL Z 120 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS Z 202 " --> pdb=" O TYR Z 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'Z' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 259 through 261 current: chain 'Z' and resid 284 through 312 removed outlier: 6.362A pdb=" N GLY Z 324 " --> pdb=" O PRO Z 299 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN Z 301 " --> pdb=" O ILE Z 322 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE Z 322 " --> pdb=" O ASN Z 301 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR Z 303 " --> pdb=" O GLY Z 320A" (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN Z 315 " --> pdb=" O ILE Z 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 315 through 324 current: chain 'Z' and resid 381 through 385 removed outlier: 4.248A pdb=" N PHE Z 382 " --> pdb=" O LYS Z 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 413 through 421 current: chain 'Z' and resid 465 through 470 570 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6234 1.35 - 1.48: 5542 1.48 - 1.61: 8732 1.61 - 1.74: 0 1.74 - 1.86: 156 Bond restraints: 20664 Sorted by residual: bond pdb=" C1 MAN b 5 " pdb=" C2 MAN b 5 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 MAN c 4 " pdb=" C2 MAN c 4 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN K 5 " pdb=" C2 MAN K 5 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 MAN k 5 " pdb=" C2 MAN k 5 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C2 BMA K 3 " pdb=" C3 BMA K 3 " ideal model delta sigma weight residual 1.544 1.506 0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 20659 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.85: 406 105.85 - 112.93: 12073 112.93 - 120.01: 6527 120.01 - 127.10: 8788 127.10 - 134.18: 262 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C GLN Z 432 " pdb=" CA GLN Z 432 " pdb=" CB GLN Z 432 " ideal model delta sigma weight residual 117.23 110.56 6.67 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CA CYS X 247 " pdb=" CB CYS X 247 " pdb=" SG CYS X 247 " ideal model delta sigma weight residual 114.40 123.81 -9.41 2.30e+00 1.89e-01 1.67e+01 angle pdb=" CA CYS Z 247 " pdb=" CB CYS Z 247 " pdb=" SG CYS Z 247 " ideal model delta sigma weight residual 114.40 123.23 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA GLN Z 432 " pdb=" C GLN Z 432 " pdb=" N ALA Z 433 " ideal model delta sigma weight residual 119.98 116.89 3.09 8.50e-01 1.38e+00 1.32e+01 angle pdb=" CA PRO X 206 " pdb=" N PRO X 206 " pdb=" CD PRO X 206 " ideal model delta sigma weight residual 112.00 107.35 4.65 1.40e+00 5.10e-01 1.10e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 13215 21.83 - 43.66: 572 43.66 - 65.49: 118 65.49 - 87.32: 84 87.32 - 109.15: 39 Dihedral angle restraints: 14028 sinusoidal: 7248 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS X 54 " pdb=" SG CYS X 54 " pdb=" SG CYS X 74 " pdb=" CB CYS X 74 " ideal model delta sinusoidal sigma weight residual 93.00 20.15 72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS Z 378 " pdb=" SG CYS Z 378 " pdb=" SG CYS Z 445 " pdb=" CB CYS Z 445 " ideal model delta sinusoidal sigma weight residual -86.00 -157.87 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS Y 378 " pdb=" SG CYS Y 378 " pdb=" SG CYS Y 445 " pdb=" CB CYS Y 445 " ideal model delta sinusoidal sigma weight residual -86.00 -155.58 69.58 1 1.00e+01 1.00e-02 6.25e+01 ... (remaining 14025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2839 0.058 - 0.116: 596 0.116 - 0.174: 101 0.174 - 0.231: 0 0.231 - 0.289: 10 Chirality restraints: 3546 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN Z 444 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA k 3 " pdb=" C4 BMA k 3 " pdb=" C6 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3543 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS X 205 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO X 206 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO X 206 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO X 206 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 75 " 0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO Y 76 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO Y 76 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO Y 76 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 32 " 0.016 2.00e-02 2.50e+03 1.45e-02 5.26e+00 pdb=" CG TRP L 32 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 32 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP L 32 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 32 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 32 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 32 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 32 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 32 " 0.004 2.00e-02 2.50e+03 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1026 2.73 - 3.27: 18705 3.27 - 3.82: 32183 3.82 - 4.36: 37999 4.36 - 4.90: 67032 Nonbonded interactions: 156945 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" OG SER A 82 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR X 37 " pdb=" OG1 THR X 499 " model vdw 2.208 2.440 nonbonded pdb=" OG SER H 69 " pdb=" OG SER H 82 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR A 74 " pdb=" OG SER A 77 " model vdw 2.249 2.440 nonbonded pdb=" OE1 GLU D 84 " pdb=" O4 MAN K 6 " model vdw 2.263 2.440 ... (remaining 156940 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 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'b' selection = chain 'k' } ncs_group { reference = chain 'M' selection = chain 'c' selection = chain 'l' } ncs_group { reference = chain 'P' selection = chain 'd' selection = chain 'm' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'X' selection = (chain 'Y' and (resid 33 through 504 or resid 701 through 708)) selection = (chain 'Z' and (resid 33 through 504 or resid 701 through 708)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 53.550 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.170 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:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.005 0.086 20664 Z= 0.327 Angle : 0.761 9.409 28056 Z= 0.347 Chirality : 0.050 0.289 3546 Planarity : 0.005 0.100 3375 Dihedral : 14.805 109.151 9552 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.49 (0.17), residues: 2316 helix: 1.41 (0.28), residues: 384 sheet: 0.96 (0.20), residues: 666 loop : -0.33 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 32 HIS 0.007 0.001 HIS Y 374 PHE 0.024 0.002 PHE R 522 TYR 0.022 0.001 TYR L 91 ARG 0.014 0.001 ARG X 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.007 Fit side-chains REVERT: D 116 MET cc_start: 0.8146 (mtp) cc_final: 0.7941 (mtm) REVERT: H 110 LEU cc_start: 0.8619 (mt) cc_final: 0.8403 (mt) REVERT: X 211 ASP cc_start: 0.7264 (t0) cc_final: 0.7059 (t0) REVERT: X 326 ILE cc_start: 0.8364 (mm) cc_final: 0.8109 (mp) REVERT: X 457 ASP cc_start: 0.7378 (t0) cc_final: 0.7158 (t0) REVERT: X 466 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7139 (tp30) REVERT: Y 111 LEU cc_start: 0.8044 (tt) cc_final: 0.7829 (tp) REVERT: Y 207 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7260 (mtmm) REVERT: Y 231 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7472 (mtpp) REVERT: Y 347 GLU cc_start: 0.7255 (tp30) cc_final: 0.6985 (tp30) REVERT: Y 443 ILE cc_start: 0.8399 (mm) cc_final: 0.8172 (mp) REVERT: Y 477 ASP cc_start: 0.7908 (m-30) cc_final: 0.7678 (m-30) REVERT: Z 123 THR cc_start: 0.8421 (t) cc_final: 0.8182 (p) REVERT: Z 168 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7916 (mmmm) REVERT: Z 211 ASP cc_start: 0.7379 (t0) cc_final: 0.7179 (t0) REVERT: Z 240 LYS cc_start: 0.7675 (mppt) cc_final: 0.7416 (mtmm) outliers start: 0 outliers final: 1 residues processed: 403 average time/residue: 1.4004 time to fit residues: 632.2832 Evaluate side-chains 375 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN X 114 GLN X 425 ASN Y 105 GLN ** Y 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 98 ASN Z 169 GLN Z 315 GLN Z 474 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20664 Z= 0.224 Angle : 0.541 7.465 28056 Z= 0.270 Chirality : 0.044 0.199 3546 Planarity : 0.004 0.081 3375 Dihedral : 10.786 83.207 5210 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.79 % Allowed : 8.14 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2316 helix: 1.92 (0.27), residues: 387 sheet: 0.92 (0.19), residues: 720 loop : -0.25 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.007 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.019 0.001 TYR L 91 ARG 0.006 0.000 ARG X 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 384 time to evaluate : 2.042 Fit side-chains REVERT: A 125 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8084 (p) REVERT: S 606 THR cc_start: 0.8296 (t) cc_final: 0.8094 (p) REVERT: X 211 ASP cc_start: 0.7294 (t0) cc_final: 0.7054 (t0) REVERT: X 389 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8318 (ttmm) REVERT: X 457 ASP cc_start: 0.7369 (t0) cc_final: 0.7151 (t0) REVERT: X 466 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7154 (tp30) REVERT: Y 111 LEU cc_start: 0.7990 (tt) cc_final: 0.7780 (tp) REVERT: Y 231 LYS cc_start: 0.7692 (mtpp) cc_final: 0.7491 (mtpp) REVERT: Y 347 GLU cc_start: 0.7293 (tp30) cc_final: 0.6957 (tp30) REVERT: Y 443 ILE cc_start: 0.8363 (mm) cc_final: 0.8159 (OUTLIER) REVERT: Z 103 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: Z 105 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7332 (tp40) REVERT: Z 168 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7918 (mmmm) REVERT: Z 381 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7111 (mm-30) REVERT: Z 426 MET cc_start: 0.5505 (mtt) cc_final: 0.5042 (mtt) outliers start: 37 outliers final: 17 residues processed: 391 average time/residue: 1.3308 time to fit residues: 586.2130 Evaluate side-chains 388 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 369 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 210 optimal weight: 0.0170 chunk 227 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN X 425 ASN ** Y 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20664 Z= 0.185 Angle : 0.509 6.625 28056 Z= 0.255 Chirality : 0.044 0.243 3546 Planarity : 0.004 0.083 3375 Dihedral : 9.032 72.985 5208 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.10 % Rotamer: Outliers : 2.42 % Allowed : 9.93 % Favored : 87.65 % 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: 0.85 (0.18), residues: 2316 helix: 2.39 (0.28), residues: 369 sheet: 0.82 (0.19), residues: 744 loop : -0.13 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 32 HIS 0.009 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.015 0.001 TYR L 91 ARG 0.008 0.000 ARG Z 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 370 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8127 (p) REVERT: X 211 ASP cc_start: 0.7276 (t0) cc_final: 0.7036 (t0) REVERT: X 326 ILE cc_start: 0.8353 (mm) cc_final: 0.8137 (mp) REVERT: X 389 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8314 (ttmm) REVERT: X 457 ASP cc_start: 0.7326 (t0) cc_final: 0.7124 (t0) REVERT: X 466 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7121 (tp30) REVERT: Y 111 LEU cc_start: 0.7997 (tt) cc_final: 0.7792 (tp) REVERT: Y 231 LYS cc_start: 0.7660 (mtpp) cc_final: 0.7422 (mtpp) REVERT: Y 443 ILE cc_start: 0.8364 (mm) cc_final: 0.8134 (OUTLIER) REVERT: Y 503 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7338 (mtm-85) REVERT: Z 230 ASP cc_start: 0.7524 (t0) cc_final: 0.7160 (t0) REVERT: Z 321 ASP cc_start: 0.7506 (t0) cc_final: 0.7253 (t70) REVERT: Z 426 MET cc_start: 0.5691 (mtt) cc_final: 0.5185 (mtt) outliers start: 50 outliers final: 25 residues processed: 384 average time/residue: 1.2999 time to fit residues: 564.3471 Evaluate side-chains 397 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 371 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain T residue 589 ASP Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 303 THR Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 316 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** X 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 169 GLN Z 183 GLN Z 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20664 Z= 0.282 Angle : 0.550 7.294 28056 Z= 0.275 Chirality : 0.045 0.255 3546 Planarity : 0.004 0.082 3375 Dihedral : 8.502 69.118 5208 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 2.76 % Allowed : 11.63 % Favored : 85.61 % 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: 0.80 (0.18), residues: 2316 helix: 2.10 (0.28), residues: 387 sheet: 1.02 (0.20), residues: 693 loop : -0.23 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 PHE 0.014 0.002 PHE Y 176 TYR 0.017 0.001 TYR E 91 ARG 0.010 0.000 ARG Z 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 388 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: A 125 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8167 (p) REVERT: E 48 ILE cc_start: 0.8010 (mm) cc_final: 0.7809 (mp) REVERT: H 67 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7879 (tp) REVERT: X 105 GLN cc_start: 0.8335 (tp40) cc_final: 0.8119 (tp-100) REVERT: X 211 ASP cc_start: 0.7295 (t0) cc_final: 0.7053 (t0) REVERT: X 457 ASP cc_start: 0.7343 (t0) cc_final: 0.7140 (t0) REVERT: Y 443 ILE cc_start: 0.8362 (mm) cc_final: 0.8152 (mp) REVERT: Y 503 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7355 (mtm-85) REVERT: Z 161 MET cc_start: 0.7989 (mmm) cc_final: 0.7774 (mmm) REVERT: Z 240 LYS cc_start: 0.7747 (mppt) cc_final: 0.7486 (mtmm) REVERT: Z 321 ASP cc_start: 0.7494 (t0) cc_final: 0.7257 (t0) REVERT: Z 381 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7013 (mm-30) REVERT: Z 426 MET cc_start: 0.5837 (mtt) cc_final: 0.5346 (mtt) outliers start: 57 outliers final: 35 residues processed: 404 average time/residue: 1.3042 time to fit residues: 594.1648 Evaluate side-chains 415 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 377 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 303 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN X 98 ASN X 203 GLN Y 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20664 Z= 0.312 Angle : 0.574 7.742 28056 Z= 0.286 Chirality : 0.046 0.256 3546 Planarity : 0.004 0.083 3375 Dihedral : 8.190 65.497 5208 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 3.15 % Allowed : 12.89 % Favored : 83.96 % 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: 0.80 (0.18), residues: 2316 helix: 2.08 (0.28), residues: 387 sheet: 0.95 (0.19), residues: 741 loop : -0.24 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 32 HIS 0.008 0.001 HIS Y 375 PHE 0.014 0.002 PHE Y 176 TYR 0.018 0.002 TYR E 91 ARG 0.009 0.001 ARG X 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 370 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8186 (p) REVERT: C 91 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6019 (m-10) REVERT: H 67 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7876 (tp) REVERT: T 616 ASN cc_start: 0.7567 (t0) cc_final: 0.7307 (t0) REVERT: X 211 ASP cc_start: 0.7315 (t0) cc_final: 0.7069 (t0) REVERT: X 389 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8240 (ttmm) REVERT: Y 443 ILE cc_start: 0.8379 (mm) cc_final: 0.8173 (mp) REVERT: Y 503 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7352 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7370 (tp40) REVERT: Z 161 MET cc_start: 0.7911 (mmm) cc_final: 0.7691 (mmm) REVERT: Z 240 LYS cc_start: 0.7748 (mppt) cc_final: 0.7501 (mtmm) REVERT: Z 321 ASP cc_start: 0.7488 (t0) cc_final: 0.7236 (t70) REVERT: Z 381 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6978 (mm-30) REVERT: Z 426 MET cc_start: 0.5920 (mtt) cc_final: 0.5425 (mtt) REVERT: Z 475 ILE cc_start: 0.8320 (tp) cc_final: 0.8077 (tp) outliers start: 65 outliers final: 46 residues processed: 392 average time/residue: 1.3231 time to fit residues: 583.9323 Evaluate side-chains 410 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 359 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 207 LYS Chi-restraints excluded: chain Y residue 208 ILE Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 303 THR Chi-restraints excluded: chain Y residue 316 MET Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 377 ASN Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 chunk 223 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Y 169 GLN Y 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20664 Z= 0.209 Angle : 0.527 6.977 28056 Z= 0.264 Chirality : 0.044 0.262 3546 Planarity : 0.004 0.086 3375 Dihedral : 7.777 62.584 5208 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 2.57 % Allowed : 14.58 % Favored : 82.85 % 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: 0.88 (0.18), residues: 2316 helix: 2.41 (0.28), residues: 369 sheet: 0.94 (0.19), residues: 729 loop : -0.17 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 32 HIS 0.009 0.001 HIS Y 375 PHE 0.012 0.001 PHE X 53 TYR 0.014 0.001 TYR E 91 ARG 0.010 0.000 ARG X 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 357 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.8420 (m) cc_final: 0.8083 (t) REVERT: A 125 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8239 (p) REVERT: H 67 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7877 (tp) REVERT: L 104 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7525 (p) REVERT: T 601 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8366 (mtpp) REVERT: X 211 ASP cc_start: 0.7314 (t0) cc_final: 0.7062 (t0) REVERT: X 389 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8240 (ttmm) REVERT: Y 443 ILE cc_start: 0.8372 (mm) cc_final: 0.8166 (mp) REVERT: Y 503 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7439 (mtm-85) REVERT: Z 161 MET cc_start: 0.7863 (mmm) cc_final: 0.7651 (mmm) REVERT: Z 321 ASP cc_start: 0.7472 (t0) cc_final: 0.7231 (t0) REVERT: Z 326 ILE cc_start: 0.8338 (pt) cc_final: 0.7862 (mm) REVERT: Z 381 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7079 (mm-30) REVERT: Z 426 MET cc_start: 0.5849 (mtt) cc_final: 0.5387 (mtt) outliers start: 53 outliers final: 37 residues processed: 378 average time/residue: 1.3063 time to fit residues: 556.7604 Evaluate side-chains 399 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 357 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain T residue 589 ASP Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 316 MET Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 222 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 43 GLN L 38 GLN T 577 GLN Y 375 HIS Z 169 GLN Z 343 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20664 Z= 0.354 Angle : 0.602 7.899 28056 Z= 0.299 Chirality : 0.046 0.253 3546 Planarity : 0.005 0.085 3375 Dihedral : 7.922 63.001 5208 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 2.96 % Allowed : 14.58 % Favored : 82.46 % 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: 0.77 (0.18), residues: 2316 helix: 2.30 (0.28), residues: 369 sheet: 0.93 (0.19), residues: 720 loop : -0.28 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 479 HIS 0.010 0.001 HIS Y 375 PHE 0.012 0.002 PHE X 53 TYR 0.020 0.002 TYR E 91 ARG 0.012 0.001 ARG X 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 372 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.8491 (m) cc_final: 0.8151 (t) REVERT: A 125 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8243 (p) REVERT: H 67 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7868 (tp) REVERT: H 121 TRP cc_start: 0.8876 (m100) cc_final: 0.8586 (m100) REVERT: T 601 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: X 211 ASP cc_start: 0.7326 (t0) cc_final: 0.7066 (t0) REVERT: X 389 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8214 (ttmm) REVERT: Y 111 LEU cc_start: 0.8010 (tt) cc_final: 0.7752 (tp) REVERT: Y 422 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: Y 427 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7769 (m100) REVERT: Y 503 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7304 (mtm-85) REVERT: Z 161 MET cc_start: 0.7886 (mmm) cc_final: 0.7671 (mmm) REVERT: Z 240 LYS cc_start: 0.7766 (mppt) cc_final: 0.7512 (mtmm) REVERT: Z 321 ASP cc_start: 0.7474 (t0) cc_final: 0.7227 (t70) REVERT: Z 326 ILE cc_start: 0.8370 (pt) cc_final: 0.7887 (mm) REVERT: Z 381 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7126 (mm-30) REVERT: Z 426 MET cc_start: 0.5978 (mtt) cc_final: 0.5538 (mtt) outliers start: 61 outliers final: 44 residues processed: 397 average time/residue: 1.2832 time to fit residues: 575.9229 Evaluate side-chains 418 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 368 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain T residue 660 LEU Chi-restraints excluded: chain X residue 201 ILE Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 201 ILE Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 303 THR Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 377 ASN Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 132 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 38 GLN T 577 GLN Y 169 GLN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20664 Z= 0.193 Angle : 0.543 7.165 28056 Z= 0.270 Chirality : 0.044 0.246 3546 Planarity : 0.004 0.083 3375 Dihedral : 7.520 60.577 5208 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.88 % Rotamer: Outliers : 2.81 % Allowed : 15.31 % Favored : 81.88 % 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: 0.82 (0.18), residues: 2316 helix: 2.40 (0.28), residues: 369 sheet: 0.80 (0.19), residues: 765 loop : -0.19 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 32 HIS 0.011 0.001 HIS Y 375 PHE 0.013 0.001 PHE X 53 TYR 0.013 0.001 TYR E 91 ARG 0.013 0.000 ARG X 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 370 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 THR cc_start: 0.8161 (t) cc_final: 0.7925 (t) REVERT: A 100 THR cc_start: 0.8414 (m) cc_final: 0.8071 (t) REVERT: A 106 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7776 (ttpp) REVERT: H 67 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7869 (tp) REVERT: T 601 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: X 211 ASP cc_start: 0.7319 (t0) cc_final: 0.7060 (t0) REVERT: X 389 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8229 (ttmm) REVERT: Y 427 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7751 (m100) REVERT: Y 503 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7335 (mtm-85) REVERT: Z 240 LYS cc_start: 0.7727 (mppt) cc_final: 0.7477 (mtmm) REVERT: Z 321 ASP cc_start: 0.7473 (t0) cc_final: 0.7220 (t0) REVERT: Z 326 ILE cc_start: 0.8355 (pt) cc_final: 0.7890 (mm) REVERT: Z 381 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7114 (mm-30) REVERT: Z 426 MET cc_start: 0.5846 (mtt) cc_final: 0.5489 (mtt) outliers start: 58 outliers final: 37 residues processed: 391 average time/residue: 1.3260 time to fit residues: 584.4581 Evaluate side-chains 409 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 367 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 592 PHE Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain T residue 660 LEU Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 303 THR Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 0.0000 chunk 187 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 206 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN T 577 GLN Y 169 GLN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20664 Z= 0.167 Angle : 0.526 7.867 28056 Z= 0.262 Chirality : 0.043 0.244 3546 Planarity : 0.004 0.079 3375 Dihedral : 7.203 59.754 5208 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 2.18 % Allowed : 16.23 % Favored : 81.59 % 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: 0.90 (0.18), residues: 2316 helix: 2.50 (0.28), residues: 369 sheet: 0.83 (0.19), residues: 753 loop : -0.11 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 32 HIS 0.010 0.001 HIS Y 375 PHE 0.014 0.001 PHE X 53 TYR 0.013 0.001 TYR E 91 ARG 0.013 0.000 ARG Z 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 371 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 THR cc_start: 0.8158 (t) cc_final: 0.7938 (t) REVERT: A 100 THR cc_start: 0.8363 (m) cc_final: 0.8017 (t) REVERT: D 55 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7458 (mmtt) REVERT: H 67 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7866 (tp) REVERT: L 87 TYR cc_start: 0.8266 (m-80) cc_final: 0.7840 (m-80) REVERT: X 265 LEU cc_start: 0.8676 (mt) cc_final: 0.8375 (mp) REVERT: X 389 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8237 (ttmm) REVERT: Y 127 VAL cc_start: 0.8422 (t) cc_final: 0.8194 (p) REVERT: Y 427 TRP cc_start: 0.8031 (OUTLIER) cc_final: 0.7725 (m100) REVERT: Y 503 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7358 (mtm-85) REVERT: Z 111 LEU cc_start: 0.7959 (tt) cc_final: 0.7747 (tm) REVERT: Z 321 ASP cc_start: 0.7431 (t0) cc_final: 0.7156 (t0) REVERT: Z 326 ILE cc_start: 0.8373 (pt) cc_final: 0.7953 (mm) REVERT: Z 381 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7113 (mm-30) REVERT: Z 426 MET cc_start: 0.5744 (mtt) cc_final: 0.5389 (mtt) outliers start: 45 outliers final: 29 residues processed: 390 average time/residue: 1.2842 time to fit residues: 565.7707 Evaluate side-chains 401 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 369 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain S residue 592 PHE Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 104 optimal weight: 0.0980 chunk 152 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN Y 203 GLN Y 375 HIS Z 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20664 Z= 0.216 Angle : 0.549 8.217 28056 Z= 0.272 Chirality : 0.044 0.243 3546 Planarity : 0.004 0.082 3375 Dihedral : 7.186 60.220 5208 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 1.84 % Allowed : 16.86 % Favored : 81.30 % 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: 0.89 (0.18), residues: 2316 helix: 2.45 (0.28), residues: 369 sheet: 0.84 (0.19), residues: 753 loop : -0.13 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 32 HIS 0.010 0.001 HIS Y 375 PHE 0.014 0.001 PHE X 53 TYR 0.014 0.001 TYR E 91 ARG 0.015 0.001 ARG Z 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 368 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7320 (mp10) cc_final: 0.6244 (mp10) REVERT: A 74 THR cc_start: 0.8163 (t) cc_final: 0.7933 (t) REVERT: D 55 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7468 (mmtt) REVERT: H 67 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7870 (tp) REVERT: L 87 TYR cc_start: 0.8268 (m-80) cc_final: 0.7917 (m-80) REVERT: T 601 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8366 (mtpp) REVERT: X 211 ASP cc_start: 0.7328 (t0) cc_final: 0.7075 (t0) REVERT: X 265 LEU cc_start: 0.8679 (mt) cc_final: 0.8372 (mp) REVERT: X 389 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8204 (ttmm) REVERT: Y 111 LEU cc_start: 0.7985 (tt) cc_final: 0.7713 (tp) REVERT: Y 127 VAL cc_start: 0.8429 (t) cc_final: 0.8176 (p) REVERT: Y 427 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7705 (m100) REVERT: Y 503 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7241 (mtm-85) REVERT: Z 321 ASP cc_start: 0.7434 (t0) cc_final: 0.7149 (t0) REVERT: Z 326 ILE cc_start: 0.8370 (pt) cc_final: 0.7952 (mm) REVERT: Z 381 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7135 (mm-30) REVERT: Z 426 MET cc_start: 0.5788 (mtt) cc_final: 0.5439 (mtt) REVERT: Z 502 LYS cc_start: 0.7952 (tttp) cc_final: 0.7598 (mtpp) outliers start: 38 outliers final: 31 residues processed: 386 average time/residue: 1.3421 time to fit residues: 583.8553 Evaluate side-chains 400 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 365 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain S residue 592 PHE Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 234 ASN Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 167 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 234 ASN Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 0.0170 chunk 161 optimal weight: 0.9980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN Y 375 HIS Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102508 restraints weight = 30004.855| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.44 r_work: 0.3177 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20664 Z= 0.222 Angle : 0.553 8.484 28056 Z= 0.274 Chirality : 0.044 0.244 3546 Planarity : 0.004 0.081 3375 Dihedral : 7.137 60.186 5208 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 2.08 % Allowed : 16.62 % Favored : 81.30 % 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: 0.88 (0.18), residues: 2316 helix: 2.45 (0.28), residues: 369 sheet: 0.84 (0.19), residues: 753 loop : -0.14 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP L 32 HIS 0.010 0.001 HIS Y 375 PHE 0.016 0.001 PHE X 159 TYR 0.014 0.001 TYR E 91 ARG 0.014 0.001 ARG Z 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8623.45 seconds wall clock time: 151 minutes 25.47 seconds (9085.47 seconds total)