Starting phenix.real_space_refine on Wed Feb 21 20:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtk_32789/02_2024/7wtk_32789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtk_32789/02_2024/7wtk_32789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtk_32789/02_2024/7wtk_32789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtk_32789/02_2024/7wtk_32789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtk_32789/02_2024/7wtk_32789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtk_32789/02_2024/7wtk_32789.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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 135 5.16 5 C 20282 2.51 5 N 5239 2.21 5 O 6239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 663": "OE1" <-> "OE2" Residue "C PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C ASP 747": "OD1" <-> "OD2" Residue "C PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1019": "OE1" <-> "OE2" Residue "C TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ASP 430": "OD1" <-> "OD2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 86": "OD1" <-> "OD2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31895 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "G" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.23, per 1000 atoms: 0.51 Number of scatterers: 31895 At special positions: 0 Unit cell: (156.22, 173.34, 241.82, 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 135 16.00 O 6239 8.00 N 5239 7.00 C 20282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 434 " distance=2.04 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 527 " distance=2.04 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 651 " distance=2.03 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 762 " distance=2.01 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C1034 " - pdb=" SG CYS C1045 " distance=2.03 Simple disulfide: pdb=" SG CYS C1084 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 434 " distance=2.04 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 527 " distance=2.07 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 651 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 762 " distance=2.05 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B1034 " - pdb=" SG CYS B1045 " distance=2.03 Simple disulfide: pdb=" SG CYS B1084 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 434 " distance=2.04 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 651 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 673 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 762 " distance=2.01 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 751 " distance=2.03 Simple disulfide: pdb=" SG CYS A1034 " - pdb=" SG CYS A1045 " distance=2.03 Simple disulfide: pdb=" SG CYS A1084 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " 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=8, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A1201 " - " ASN A1160 " " NAG A1202 " - " ASN A 125 " " NAG A1203 " - " ASN A 145 " " NAG A1204 " - " ASN A 17 " " NAG A1205 " - " ASN A 61 " " NAG A1206 " - " ASN A 605 " " NAG A1207 " - " ASN A 659 " " NAG A1208 " - " ASN A 618 " " NAG A1209 " - " ASN A 711 " " NAG B1202 " - " ASN B1160 " " NAG B1203 " - " ASN B 125 " " NAG B1204 " - " ASN B 145 " " NAG B1205 " - " ASN B 17 " " NAG B1206 " - " ASN B 61 " " NAG B1207 " - " ASN B 605 " " NAG B1208 " - " ASN B 659 " " NAG B1209 " - " ASN B 618 " " NAG B1210 " - " ASN B 711 " " NAG C1201 " - " ASN C1160 " " NAG C1204 " - " ASN C 61 " " NAG C1206 " - " ASN C 605 " " NAG C1207 " - " ASN C 659 " " NAG C1208 " - " ASN C 618 " " NAG C1209 " - " ASN C 711 " " NAG D 1 " - " ASN C 719 " " NAG F 1 " - " ASN C 803 " " NAG M 1 " - " ASN C1100 " " NAG N 1 " - " ASN C1136 " " NAG Q 1 " - " ASN B 719 " " NAG S 1 " - " ASN B 803 " " NAG T 1 " - " ASN B1100 " " NAG U 1 " - " ASN B1136 " " NAG V 1 " - " ASN A 233 " " NAG W 1 " - " ASN A 719 " " NAG Y 1 " - " ASN A 803 " " NAG Z 1 " - " ASN A1100 " " NAG a 1 " - " ASN A1136 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 6.2 seconds 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 63 sheets defined 18.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.803A pdb=" N LEU C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 739 through 745 removed outlier: 3.737A pdb=" N TYR C 743 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 757 removed outlier: 3.922A pdb=" N ASN C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 756 " --> pdb=" O SER C 752 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN C 757 " --> pdb=" O ASN C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 785 removed outlier: 4.191A pdb=" N ASP C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 781 " --> pdb=" O ASP C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 828 removed outlier: 3.768A pdb=" N LEU C 823 " --> pdb=" O PRO C 819 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 876 removed outlier: 3.521A pdb=" N ALA C 873 " --> pdb=" O ASP C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 892 removed outlier: 3.643A pdb=" N GLY C 891 " --> pdb=" O TRP C 888 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 892 " --> pdb=" O THR C 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 888 through 892' Processing helix chain 'C' and resid 899 through 910 removed outlier: 4.318A pdb=" N ALA C 905 " --> pdb=" O PRO C 901 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN C 909 " --> pdb=" O ALA C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 3.641A pdb=" N TYR C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 3.517A pdb=" N ALA C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 938 " --> pdb=" O GLY C 934 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 941 " --> pdb=" O GLN C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 966 removed outlier: 4.019A pdb=" N VAL C 953 " --> pdb=" O LYS C 949 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 957 " --> pdb=" O VAL C 953 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 966 " --> pdb=" O ASN C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 removed outlier: 3.865A pdb=" N ILE C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 978 through 983' Processing helix chain 'C' and resid 987 through 1034 removed outlier: 3.631A pdb=" N GLU C 992 " --> pdb=" O PRO C 988 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL C 993 " --> pdb=" O PRO C 989 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 996 " --> pdb=" O GLU C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 998 " --> pdb=" O GLN C 994 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C1004 " --> pdb=" O THR C1000 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C1009 " --> pdb=" O SER C1005 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C1015 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.925A pdb=" N GLU C1146 " --> pdb=" O PRO C1142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1147' Processing helix chain 'C' and resid 1147 through 1152 removed outlier: 3.549A pdb=" N LYS C1151 " --> pdb=" O LEU C1147 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1147 through 1152' Processing helix chain 'C' and resid 1152 through 1163 removed outlier: 4.221A pdb=" N LYS C1156 " --> pdb=" O GLU C1152 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR C1157 " --> pdb=" O GLU C1153 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C1158 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C1159 " --> pdb=" O ASP C1155 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C1160 " --> pdb=" O LYS C1156 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C1161 " --> pdb=" O TYR C1157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C1162 " --> pdb=" O PHE C1158 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1152 through 1163' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.982A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.593A pdb=" N LYS B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 removed outlier: 3.745A pdb=" N VAL B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.026A pdb=" N VAL B 369 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.637A pdb=" N LEU B 389 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN B 390 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 392 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.383A pdb=" N ARG B 410 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 removed outlier: 3.911A pdb=" N TYR B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 424' Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.809A pdb=" N TYR B 638 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 639 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.530A pdb=" N ILE B 744 " --> pdb=" O CYS B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 757 removed outlier: 3.856A pdb=" N ASN B 753 " --> pdb=" O THR B 749 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 754 " --> pdb=" O GLU B 750 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 757 " --> pdb=" O ASN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 779 removed outlier: 3.531A pdb=" N ASP B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 778 " --> pdb=" O VAL B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 828 removed outlier: 3.899A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 881 removed outlier: 3.513A pdb=" N SER B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 removed outlier: 3.575A pdb=" N ALA B 892 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 909 removed outlier: 3.691A pdb=" N MET B 904 " --> pdb=" O PHE B 900 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 909 " --> pdb=" O ALA B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.901A pdb=" N TYR B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 removed outlier: 3.641A pdb=" N GLY B 934 " --> pdb=" O ASN B 930 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 940 removed outlier: 3.632A pdb=" N SER B 939 " --> pdb=" O LYS B 935 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 940 " --> pdb=" O ILE B 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 935 through 940' Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.666A pdb=" N VAL B 953 " --> pdb=" O LYS B 949 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 970 No H-bonds generated for 'chain 'B' and resid 968 through 970' Processing helix chain 'B' and resid 979 through 986 removed outlier: 4.156A pdb=" N PHE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1034 removed outlier: 3.747A pdb=" N GLN B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 998 " --> pdb=" O GLN B 994 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER B1032 " --> pdb=" O ALA B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1120 No H-bonds generated for 'chain 'B' and resid 1118 through 1120' Processing helix chain 'B' and resid 1143 through 1148 Processing helix chain 'B' and resid 1150 through 1158 removed outlier: 3.599A pdb=" N TYR B1157 " --> pdb=" O GLU B1153 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B1158 " --> pdb=" O LEU B1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.800A pdb=" N ARG A 410 " --> pdb=" O ASP A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.589A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.928A pdb=" N ILE A 744 " --> pdb=" O CYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.588A pdb=" N ASN A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.715A pdb=" N GLN A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 775 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 778 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 828 removed outlier: 3.734A pdb=" N LEU A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.528A pdb=" N SER A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 880 " --> pdb=" O THR A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.520A pdb=" N ALA A 892 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 910 removed outlier: 4.545A pdb=" N ALA A 905 " --> pdb=" O PRO A 901 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 908 " --> pdb=" O MET A 904 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 910 " --> pdb=" O TYR A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.577A pdb=" N TYR A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 921 through 941 removed outlier: 3.538A pdb=" N ILE A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 966 removed outlier: 3.529A pdb=" N ASP A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 957 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 970 removed outlier: 3.577A pdb=" N SER A 970 " --> pdb=" O GLN A 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 970' Processing helix chain 'A' and resid 990 through 1033 removed outlier: 3.547A pdb=" N ARG A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A1015 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1147 through 1163 removed outlier: 3.837A pdb=" N LYS A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A1152 " --> pdb=" O ASP A1148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A1158 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A1161 " --> pdb=" O TYR A1157 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.807A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.882A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.368A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN C 61 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 271 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 266 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.781A pdb=" N ASP C 289 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.585A pdb=" N ARG C 236 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 107 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 105 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314 removed outlier: 3.747A pdb=" N THR C 601 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 358 through 360 removed outlier: 3.512A pdb=" N LYS C 358 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 399 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 360 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 396 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 518 " --> pdb=" O ASN C 396 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 513 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C 436 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 515 " --> pdb=" O CYS C 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 404 through 405 Processing sheet with id=AA7, first strand: chain 'C' and resid 454 through 456 Processing sheet with id=AA8, first strand: chain 'C' and resid 553 through 556 removed outlier: 3.585A pdb=" N VAL C 553 " --> pdb=" O THR C 590 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 590 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 645 through 646 Processing sheet with id=AB1, first strand: chain 'C' and resid 656 through 657 removed outlier: 6.146A pdb=" N GLU C 656 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR C 698 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 695 " --> pdb=" O SER C 675 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 672 " --> pdb=" O ILE C 668 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 666 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 715 through 717 Processing sheet with id=AB3, first strand: chain 'C' and resid 720 through 721 Processing sheet with id=AB4, first strand: chain 'C' and resid 724 through 730 removed outlier: 3.584A pdb=" N GLU C 727 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 737 through 738 Processing sheet with id=AB6, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 3.785A pdb=" N VAL C1096 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 3.564A pdb=" N CYS C1084 " --> pdb=" O VAL C1135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1088 through 1092 removed outlier: 4.599A pdb=" N ALA C1089 " --> pdb=" O SER C1125 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C1125 " --> pdb=" O ALA C1089 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.998A pdb=" N SER H 59 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.707A pdb=" N SER L 64 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 45 through 49 removed outlier: 4.305A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP L 36 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA L 91 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.961A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR B 63 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 269 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.879A pdb=" N ASP B 289 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'B' and resid 90 through 96 removed outlier: 3.937A pdb=" N GLU B 188 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 226 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.696A pdb=" N GLU B 132 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 313 through 321 removed outlier: 5.410A pdb=" N ILE B 314 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR B 601 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN B 316 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 599 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 318 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 597 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 596 " --> pdb=" O GLN B 615 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 645 " --> pdb=" O LEU B 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AD3, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.606A pdb=" N ASN B 336 " --> pdb=" O VAL B 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 356 through 360 removed outlier: 4.221A pdb=" N ASN B 356 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 401 " --> pdb=" O ASN B 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 358 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 360 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 397 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 400 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AD6, first strand: chain 'B' and resid 553 through 556 removed outlier: 3.548A pdb=" N THR B 590 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 588 " --> pdb=" O THR B 555 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 656 through 657 removed outlier: 6.129A pdb=" N GLU B 656 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR B 698 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 673 " --> pdb=" O TYR B 697 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 713 through 717 removed outlier: 4.052A pdb=" N VAL B1096 " --> pdb=" O THR B1107 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B1107 " --> pdb=" O VAL B1096 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 720 through 730 removed outlier: 3.515A pdb=" N GLU B 727 " --> pdb=" O PHE B1064 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B1067 " --> pdb=" O LEU B1051 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 720 through 730 removed outlier: 3.515A pdb=" N GLU B 727 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1122 through 1127 removed outlier: 4.703A pdb=" N ALA B1089 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B1084 " --> pdb=" O VAL B1135 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.817A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASN A 61 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A 271 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 266 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP A 289 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.806A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 313 through 316 removed outlier: 3.953A pdb=" N THR A 601 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 652 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 645 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 356 through 359 removed outlier: 4.260A pdb=" N ASN A 356 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 401 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 511 " --> pdb=" O TRP A 438 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 438 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 454 through 456 Processing sheet with id=AF1, first strand: chain 'A' and resid 475 through 476 Processing sheet with id=AF2, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AF3, first strand: chain 'A' and resid 656 through 657 removed outlier: 5.794A pdb=" N GLU A 656 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR A 698 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 693 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 677 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 695 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA A 674 " --> pdb=" O PRO A 667 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 715 through 717 removed outlier: 3.530A pdb=" N LYS A1075 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 720 through 721 Processing sheet with id=AF6, first strand: chain 'A' and resid 724 through 730 removed outlier: 3.798A pdb=" N GLU A 727 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AF8, first strand: chain 'A' and resid 1083 through 1084 removed outlier: 3.630A pdb=" N CYS A1084 " --> pdb=" O VAL A1135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AG1, first strand: chain 'G' and resid 18 through 23 removed outlier: 3.724A pdb=" N CYS G 22 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 57 through 60 removed outlier: 3.629A pdb=" N ILE G 50 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.968A pdb=" N CYS I 22 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 45 through 51 removed outlier: 6.177A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AG6, first strand: chain 'J' and resid 46 through 47 removed outlier: 3.864A pdb=" N LYS J 46 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN J 38 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 46 through 47 removed outlier: 3.864A pdb=" N LYS J 46 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN J 38 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR J 87 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR J 107 " --> pdb=" O TYR J 87 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG9, first strand: chain 'K' and resid 34 through 39 removed outlier: 3.820A pdb=" N ASP K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2121 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: 13.48 Time building geometry restraints manager: 14.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5666 1.33 - 1.45: 9394 1.45 - 1.58: 17426 1.58 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 32657 Sorted by residual: bond pdb=" C PHE A 761 " pdb=" O PHE A 761 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.22e-02 6.72e+03 2.70e+01 bond pdb=" C ALA C 374 " pdb=" N PRO C 375 " ideal model delta sigma weight residual 1.337 1.387 -0.051 9.80e-03 1.04e+04 2.66e+01 bond pdb=" N VAL C 329 " pdb=" CA VAL C 329 " ideal model delta sigma weight residual 1.457 1.513 -0.056 1.15e-02 7.56e+03 2.39e+01 bond pdb=" C1 NAG A1205 " pdb=" O5 NAG A1205 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 NAG B1207 " pdb=" O5 NAG B1207 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 32652 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.61: 803 105.61 - 113.32: 17794 113.32 - 121.02: 15489 121.02 - 128.72: 10189 128.72 - 136.42: 183 Bond angle restraints: 44458 Sorted by residual: angle pdb=" CA PRO B 988 " pdb=" N PRO B 988 " pdb=" CD PRO B 988 " ideal model delta sigma weight residual 112.00 99.16 12.84 1.40e+00 5.10e-01 8.41e+01 angle pdb=" CA PRO B 944 " pdb=" N PRO B 944 " pdb=" CD PRO B 944 " ideal model delta sigma weight residual 112.00 99.25 12.75 1.40e+00 5.10e-01 8.29e+01 angle pdb=" CA PRO A 988 " pdb=" N PRO A 988 " pdb=" CD PRO A 988 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.25e+01 angle pdb=" CA PRO C 944 " pdb=" N PRO C 944 " pdb=" CD PRO C 944 " ideal model delta sigma weight residual 112.00 99.33 12.67 1.40e+00 5.10e-01 8.19e+01 angle pdb=" CA PRO A 944 " pdb=" N PRO A 944 " pdb=" CD PRO A 944 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.17e+01 ... (remaining 44453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 19044 26.62 - 53.23: 998 53.23 - 79.85: 161 79.85 - 106.47: 82 106.47 - 133.09: 22 Dihedral angle restraints: 20307 sinusoidal: 8781 harmonic: 11526 Sorted by residual: dihedral pdb=" CA ASN C 333 " pdb=" C ASN C 333 " pdb=" N ILE C 334 " pdb=" CA ILE C 334 " ideal model delta harmonic sigma weight residual 180.00 46.91 133.09 0 5.00e+00 4.00e-02 7.08e+02 dihedral pdb=" C ASN B 145 " pdb=" N ASN B 145 " pdb=" CA ASN B 145 " pdb=" CB ASN B 145 " ideal model delta harmonic sigma weight residual -122.60 -145.49 22.89 0 2.50e+00 1.60e-01 8.39e+01 dihedral pdb=" CB CYS C 664 " pdb=" SG CYS C 664 " pdb=" SG CYS C 673 " pdb=" CB CYS C 673 " ideal model delta sinusoidal sigma weight residual -86.00 -6.92 -79.08 1 1.00e+01 1.00e-02 7.78e+01 ... (remaining 20304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 5037 0.158 - 0.317: 104 0.317 - 0.475: 19 0.475 - 0.633: 3 0.633 - 0.792: 2 Chirality restraints: 5165 Sorted by residual: chirality pdb=" CA ASN B 145 " pdb=" N ASN B 145 " pdb=" C ASN B 145 " pdb=" CB ASN B 145 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -3.02 0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 5162 not shown) Planarity restraints: 5690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 900 " 0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO A 901 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO A 901 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 901 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 900 " -0.096 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO C 901 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 901 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 901 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 893 " 0.095 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO B 894 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 894 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 894 " 0.068 5.00e-02 4.00e+02 ... (remaining 5687 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 44 2.37 - 3.00: 16304 3.00 - 3.63: 44263 3.63 - 4.27: 66183 4.27 - 4.90: 109782 Nonbonded interactions: 236576 Sorted by model distance: nonbonded pdb=" OG SER A 818 " pdb=" CD PRO A 819 " model vdw 1.732 3.440 nonbonded pdb=" OG1 THR A 943 " pdb=" CD PRO A 944 " model vdw 1.739 3.440 nonbonded pdb=" OG SER C 818 " pdb=" CD PRO C 819 " model vdw 1.805 3.440 nonbonded pdb=" O GLN B 806 " pdb=" CD PRO B 819 " model vdw 1.934 3.440 nonbonded pdb=" OD1 ASP A 987 " pdb=" CD PRO A 988 " model vdw 1.977 3.440 ... (remaining 236571 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 'B' and (resid 14 through 1164 or resid 1201 through 1209)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.260 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 85.000 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 32657 Z= 0.370 Angle : 1.005 14.691 44458 Z= 0.598 Chirality : 0.066 0.792 5165 Planarity : 0.009 0.138 5653 Dihedral : 17.393 133.086 12780 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.01 % Favored : 91.53 % Rotamer: Outliers : 1.20 % Allowed : 1.37 % Favored : 97.43 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % 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: -2.94 (0.12), residues: 3933 helix: -3.24 (0.14), residues: 607 sheet: -0.36 (0.18), residues: 878 loop : -2.33 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 111 HIS 0.005 0.001 HIS H 35 PHE 0.050 0.002 PHE C 340 TYR 0.046 0.001 TYR C 28 ARG 0.009 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 50 ILE cc_start: 0.6259 (tp) cc_final: 0.5992 (tp) REVERT: B 144 LYS cc_start: 0.5221 (OUTLIER) cc_final: 0.4731 (mmmt) REVERT: B 153 GLU cc_start: 0.1280 (OUTLIER) cc_final: 0.0596 (pm20) REVERT: B 450 ASN cc_start: 0.7766 (m-40) cc_final: 0.7305 (p0) REVERT: A 155 ARG cc_start: 0.6681 (mmp80) cc_final: 0.6412 (ttp80) REVERT: A 174 MET cc_start: 0.2213 (mpp) cc_final: 0.1888 (mpp) REVERT: I 48 MET cc_start: 0.6529 (ppp) cc_final: 0.6165 (ppp) REVERT: J 87 TYR cc_start: 0.7745 (m-80) cc_final: 0.7453 (m-10) outliers start: 41 outliers final: 20 residues processed: 238 average time/residue: 0.4251 time to fit residues: 167.5590 Evaluate side-chains 179 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 PRO Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain K residue 94 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 305 optimal weight: 0.3980 chunk 118 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 416 GLN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 GLN H 35 HIS L 28 ASN L 32 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN B 951 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN K 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 32657 Z= 0.270 Angle : 0.673 11.706 44458 Z= 0.337 Chirality : 0.048 0.441 5165 Planarity : 0.005 0.069 5653 Dihedral : 13.687 124.130 5779 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 1.11 % Allowed : 9.17 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % 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: -2.35 (0.13), residues: 3933 helix: -1.48 (0.19), residues: 617 sheet: -0.40 (0.18), residues: 900 loop : -2.14 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.006 0.001 HIS C1066 PHE 0.028 0.002 PHE C 106 TYR 0.022 0.001 TYR B1069 ARG 0.005 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 340 PHE cc_start: 0.5096 (m-80) cc_final: 0.4834 (m-80) REVERT: B 144 LYS cc_start: 0.4995 (OUTLIER) cc_final: 0.4287 (mmmm) REVERT: B 150 MET cc_start: 0.5993 (mmm) cc_final: 0.5251 (tpt) REVERT: B 450 ASN cc_start: 0.7833 (m-40) cc_final: 0.7345 (p0) REVERT: B 758 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 155 ARG cc_start: 0.6585 (mmp80) cc_final: 0.6342 (ttp80) REVERT: I 48 MET cc_start: 0.6353 (ppp) cc_final: 0.6135 (ppp) REVERT: J 87 TYR cc_start: 0.7888 (m-80) cc_final: 0.7525 (m-10) outliers start: 38 outliers final: 28 residues processed: 208 average time/residue: 0.4147 time to fit residues: 143.2094 Evaluate side-chains 186 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 PRO Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 94 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 383 optimal weight: 40.0000 chunk 315 optimal weight: 0.8980 chunk 351 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 566 GLN C 806 GLN L 28 ASN B 921 ASN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 897 GLN A 930 ASN K 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 32657 Z= 0.419 Angle : 0.736 10.607 44458 Z= 0.367 Chirality : 0.050 0.450 5165 Planarity : 0.005 0.060 5653 Dihedral : 11.366 124.468 5766 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.51 % Favored : 90.39 % Rotamer: Outliers : 2.74 % Allowed : 13.69 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % 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: -2.29 (0.13), residues: 3933 helix: -0.94 (0.20), residues: 628 sheet: -0.59 (0.17), residues: 914 loop : -2.17 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 107 HIS 0.009 0.001 HIS C1066 PHE 0.048 0.002 PHE C 106 TYR 0.028 0.002 TYR B1069 ARG 0.017 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 164 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.4560 (p90) REVERT: C 455 TYR cc_start: 0.4803 (p90) cc_final: 0.4333 (p90) REVERT: B 144 LYS cc_start: 0.4654 (OUTLIER) cc_final: 0.4305 (mmmm) REVERT: B 150 MET cc_start: 0.6038 (mmm) cc_final: 0.5139 (tpt) REVERT: B 450 ASN cc_start: 0.7969 (m-40) cc_final: 0.7570 (p0) REVERT: B 758 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 155 ARG cc_start: 0.6766 (mmp80) cc_final: 0.6387 (ttp80) REVERT: A 802 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: I 48 MET cc_start: 0.6326 (ppp) cc_final: 0.6119 (ppp) outliers start: 94 outliers final: 57 residues processed: 242 average time/residue: 0.3808 time to fit residues: 155.8764 Evaluate side-chains 210 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 149 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1129 ASP Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1091 PHE Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 94 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 238 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 376 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 337 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 ASN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B 962 ASN B1108 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32657 Z= 0.172 Angle : 0.599 9.717 44458 Z= 0.295 Chirality : 0.045 0.411 5165 Planarity : 0.004 0.055 5653 Dihedral : 9.969 119.493 5757 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 1.98 % Allowed : 16.20 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3933 helix: -0.30 (0.22), residues: 614 sheet: -0.31 (0.18), residues: 857 loop : -2.06 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 107 HIS 0.003 0.000 HIS C1050 PHE 0.021 0.001 PHE C 106 TYR 0.017 0.001 TYR C 503 ARG 0.004 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 171 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.4544 (p90) REVERT: C 117 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6640 (tt) REVERT: C 333 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6836 (p0) REVERT: C 1004 GLN cc_start: 0.7805 (tp40) cc_final: 0.7603 (tm-30) REVERT: B 144 LYS cc_start: 0.4486 (OUTLIER) cc_final: 0.3996 (mttt) REVERT: B 150 MET cc_start: 0.6127 (mmm) cc_final: 0.5321 (tpt) REVERT: B 450 ASN cc_start: 0.8003 (m-40) cc_final: 0.7446 (p0) REVERT: B 634 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7694 (m) REVERT: B 758 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7571 (t80) REVERT: A 155 ARG cc_start: 0.6755 (mmp80) cc_final: 0.6411 (ttp80) REVERT: I 48 MET cc_start: 0.6374 (ppp) cc_final: 0.6139 (ppp) REVERT: J 87 TYR cc_start: 0.7976 (m-80) cc_final: 0.7664 (m-10) outliers start: 68 outliers final: 36 residues processed: 230 average time/residue: 0.4149 time to fit residues: 160.3986 Evaluate side-chains 203 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 747 ASP Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 94 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 280 optimal weight: 40.0000 chunk 155 optimal weight: 4.9990 chunk 321 optimal weight: 0.0670 chunk 260 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 192 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B1108 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32657 Z= 0.187 Angle : 0.599 10.553 44458 Z= 0.293 Chirality : 0.045 0.416 5165 Planarity : 0.004 0.054 5653 Dihedral : 9.479 119.754 5752 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 2.34 % Allowed : 17.25 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3933 helix: -0.10 (0.22), residues: 619 sheet: -0.27 (0.18), residues: 854 loop : -2.02 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 36 HIS 0.003 0.001 HIS C1066 PHE 0.021 0.001 PHE B 183 TYR 0.016 0.001 TYR B1069 ARG 0.005 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 162 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.4505 (p90) REVERT: C 117 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6677 (tt) REVERT: C 333 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.7132 (m110) REVERT: C 455 TYR cc_start: 0.6006 (p90) cc_final: 0.4860 (p90) REVERT: C 1004 GLN cc_start: 0.7859 (tp40) cc_final: 0.7639 (tm-30) REVERT: B 144 LYS cc_start: 0.4473 (OUTLIER) cc_final: 0.4031 (mttt) REVERT: B 150 MET cc_start: 0.6216 (mmm) cc_final: 0.5456 (tpt) REVERT: B 450 ASN cc_start: 0.8032 (m-40) cc_final: 0.7540 (p0) REVERT: B 634 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7703 (m) REVERT: B 758 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7634 (t80) REVERT: B 1033 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: A 155 ARG cc_start: 0.6764 (mmp80) cc_final: 0.6434 (ttp80) REVERT: I 48 MET cc_start: 0.6406 (ppp) cc_final: 0.6159 (ppp) REVERT: J 87 TYR cc_start: 0.7970 (m-80) cc_final: 0.7663 (m-10) outliers start: 80 outliers final: 49 residues processed: 233 average time/residue: 0.3951 time to fit residues: 155.8412 Evaluate side-chains 212 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 156 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain B residue 1144 GLN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 94 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 40.0000 chunk 339 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 377 optimal weight: 30.0000 chunk 313 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 31 optimal weight: 40.0000 chunk 124 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32657 Z= 0.293 Angle : 0.642 10.457 44458 Z= 0.318 Chirality : 0.047 0.431 5165 Planarity : 0.004 0.053 5653 Dihedral : 9.180 119.670 5752 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 2.77 % Allowed : 17.54 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3933 helix: -0.18 (0.22), residues: 619 sheet: -0.33 (0.18), residues: 848 loop : -2.04 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 36 HIS 0.006 0.001 HIS C1066 PHE 0.031 0.002 PHE C 106 TYR 0.021 0.001 TYR B1069 ARG 0.006 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 161 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5209 (p90) REVERT: C 117 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6770 (tt) REVERT: C 234 ILE cc_start: 0.8312 (mm) cc_final: 0.8016 (tt) REVERT: C 333 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.6978 (p0) REVERT: C 455 TYR cc_start: 0.6180 (p90) cc_final: 0.5010 (p90) REVERT: B 150 MET cc_start: 0.6155 (mmm) cc_final: 0.5446 (tpt) REVERT: B 450 ASN cc_start: 0.8096 (m-40) cc_final: 0.7631 (p0) REVERT: B 634 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7779 (m) REVERT: B 758 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7582 (t80) REVERT: B 875 TYR cc_start: 0.8483 (m-80) cc_final: 0.8222 (m-80) REVERT: B 983 PHE cc_start: 0.8914 (m-80) cc_final: 0.8664 (m-80) REVERT: B 1033 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: B 1144 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7654 (tp40) REVERT: A 155 ARG cc_start: 0.6719 (mmp80) cc_final: 0.6392 (ttp80) REVERT: I 48 MET cc_start: 0.6404 (ppp) cc_final: 0.6145 (ppp) outliers start: 95 outliers final: 67 residues processed: 241 average time/residue: 0.3935 time to fit residues: 161.9891 Evaluate side-chains 226 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 152 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain B residue 1144 GLN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 93 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 50.0000 chunk 42 optimal weight: 30.0000 chunk 214 optimal weight: 0.7980 chunk 275 optimal weight: 30.0000 chunk 213 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 375 optimal weight: 0.3980 chunk 235 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 ASN L 28 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32657 Z= 0.184 Angle : 0.592 10.719 44458 Z= 0.291 Chirality : 0.045 0.416 5165 Planarity : 0.004 0.051 5653 Dihedral : 8.719 117.580 5750 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 2.71 % Allowed : 18.39 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3933 helix: 0.06 (0.22), residues: 612 sheet: -0.25 (0.18), residues: 861 loop : -1.96 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 92 HIS 0.003 0.001 HIS C1066 PHE 0.021 0.001 PHE C 106 TYR 0.016 0.001 TYR A 367 ARG 0.006 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 166 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.4950 (p90) REVERT: C 117 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6842 (tt) REVERT: C 234 ILE cc_start: 0.8273 (mm) cc_final: 0.8049 (tt) REVERT: C 333 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6765 (p0) REVERT: C 455 TYR cc_start: 0.6206 (p90) cc_final: 0.5079 (p90) REVERT: C 1004 GLN cc_start: 0.7790 (tp40) cc_final: 0.7553 (tm-30) REVERT: B 150 MET cc_start: 0.6217 (mmm) cc_final: 0.5501 (tpt) REVERT: B 450 ASN cc_start: 0.8081 (m-40) cc_final: 0.7623 (p0) REVERT: B 634 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7757 (m) REVERT: B 758 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.7652 (t80) REVERT: B 875 TYR cc_start: 0.8432 (m-80) cc_final: 0.8160 (m-80) REVERT: B 983 PHE cc_start: 0.8856 (m-80) cc_final: 0.8586 (m-80) REVERT: B 1144 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7759 (tp40) REVERT: A 155 ARG cc_start: 0.6692 (mmp80) cc_final: 0.6394 (ttp80) REVERT: I 48 MET cc_start: 0.6340 (ppp) cc_final: 0.6077 (ppp) REVERT: J 87 TYR cc_start: 0.8022 (m-80) cc_final: 0.7782 (m-10) REVERT: K 37 TYR cc_start: 0.3649 (OUTLIER) cc_final: 0.2803 (t80) outliers start: 93 outliers final: 71 residues processed: 244 average time/residue: 0.3885 time to fit residues: 161.1581 Evaluate side-chains 234 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 156 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 995 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain B residue 1144 GLN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 37 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 256 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 295 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32657 Z= 0.236 Angle : 0.610 10.476 44458 Z= 0.300 Chirality : 0.046 0.424 5165 Planarity : 0.004 0.051 5653 Dihedral : 8.449 117.341 5750 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.51 % Rotamer: Outliers : 2.89 % Allowed : 18.68 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 3933 helix: 0.06 (0.22), residues: 620 sheet: -0.22 (0.18), residues: 862 loop : -1.98 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 92 HIS 0.004 0.001 HIS C1066 PHE 0.023 0.001 PHE C 106 TYR 0.018 0.001 TYR B1069 ARG 0.003 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 156 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.5102 (p90) REVERT: C 117 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6953 (tt) REVERT: C 333 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6698 (p0) REVERT: B 150 MET cc_start: 0.6220 (mmm) cc_final: 0.5498 (tpt) REVERT: B 450 ASN cc_start: 0.8093 (m-40) cc_final: 0.7633 (p0) REVERT: B 634 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7770 (m) REVERT: B 758 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7558 (t80) REVERT: B 875 TYR cc_start: 0.8470 (m-80) cc_final: 0.8212 (m-80) REVERT: B 951 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: B 983 PHE cc_start: 0.8853 (m-80) cc_final: 0.8580 (m-80) REVERT: B 1144 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7832 (tp40) REVERT: A 155 ARG cc_start: 0.6721 (mmp80) cc_final: 0.6407 (ttp80) REVERT: A 439 ASN cc_start: 0.5831 (OUTLIER) cc_final: 0.5563 (t0) REVERT: I 48 MET cc_start: 0.6333 (ppp) cc_final: 0.6064 (ppp) REVERT: J 87 TYR cc_start: 0.8028 (m-80) cc_final: 0.7778 (m-10) REVERT: K 37 TYR cc_start: 0.3653 (OUTLIER) cc_final: 0.2799 (t80) outliers start: 99 outliers final: 80 residues processed: 242 average time/residue: 0.3997 time to fit residues: 164.0315 Evaluate side-chains 242 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 153 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 995 ILE Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain B residue 1144 GLN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 37 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 0.0370 chunk 360 optimal weight: 20.0000 chunk 328 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 210 optimal weight: 0.0980 chunk 152 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 331 optimal weight: 0.6980 chunk 349 optimal weight: 8.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A1137 ASN ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32657 Z= 0.199 Angle : 0.596 10.568 44458 Z= 0.292 Chirality : 0.045 0.420 5165 Planarity : 0.004 0.045 5653 Dihedral : 8.177 115.893 5749 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 2.74 % Allowed : 18.68 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3933 helix: 0.29 (0.22), residues: 601 sheet: -0.22 (0.18), residues: 841 loop : -1.96 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 92 HIS 0.003 0.001 HIS C1066 PHE 0.021 0.001 PHE C 106 TYR 0.017 0.001 TYR A 367 ARG 0.008 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 160 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.4968 (p90) REVERT: C 117 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6934 (tt) REVERT: C 234 ILE cc_start: 0.8384 (mm) cc_final: 0.8131 (tt) REVERT: C 333 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6514 (p0) REVERT: C 455 TYR cc_start: 0.6343 (p90) cc_final: 0.5101 (p90) REVERT: C 1004 GLN cc_start: 0.7800 (tp40) cc_final: 0.7545 (tm-30) REVERT: B 150 MET cc_start: 0.6129 (mmm) cc_final: 0.5415 (tpt) REVERT: B 450 ASN cc_start: 0.8095 (m-40) cc_final: 0.7633 (p0) REVERT: B 634 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7784 (m) REVERT: B 758 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 875 TYR cc_start: 0.8452 (m-80) cc_final: 0.8196 (m-80) REVERT: B 983 PHE cc_start: 0.8841 (m-80) cc_final: 0.8528 (m-80) REVERT: B 1144 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7868 (tp40) REVERT: A 155 ARG cc_start: 0.6726 (mmp80) cc_final: 0.6429 (ttp80) REVERT: A 427 LEU cc_start: 0.6841 (mp) cc_final: 0.6274 (pt) REVERT: A 439 ASN cc_start: 0.6108 (OUTLIER) cc_final: 0.5885 (t0) REVERT: I 48 MET cc_start: 0.6376 (ppp) cc_final: 0.6043 (ppp) REVERT: J 87 TYR cc_start: 0.8008 (m-80) cc_final: 0.7777 (m-10) REVERT: K 37 TYR cc_start: 0.3590 (OUTLIER) cc_final: 0.2764 (t80) outliers start: 94 outliers final: 78 residues processed: 241 average time/residue: 0.3915 time to fit residues: 160.7420 Evaluate side-chains 241 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 155 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 995 ILE Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain B residue 1144 GLN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 0.9980 chunk 370 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 309 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 189 optimal weight: 0.0050 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32657 Z= 0.254 Angle : 0.617 10.467 44458 Z= 0.303 Chirality : 0.046 0.423 5165 Planarity : 0.004 0.046 5653 Dihedral : 8.053 115.919 5749 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.80 % Favored : 91.15 % Rotamer: Outliers : 2.63 % Allowed : 18.97 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3933 helix: 0.24 (0.22), residues: 607 sheet: -0.27 (0.18), residues: 838 loop : -1.98 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 36 HIS 0.005 0.001 HIS C1066 PHE 0.024 0.001 PHE C 106 TYR 0.019 0.001 TYR B1069 ARG 0.003 0.000 ARG L 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 155 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5180 (p90) REVERT: C 117 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6958 (tt) REVERT: C 234 ILE cc_start: 0.8410 (mm) cc_final: 0.8155 (tt) REVERT: C 333 ASN cc_start: 0.6873 (OUTLIER) cc_final: 0.6464 (p0) REVERT: C 455 TYR cc_start: 0.6313 (p90) cc_final: 0.5091 (p90) REVERT: C 1004 GLN cc_start: 0.7836 (tp40) cc_final: 0.7571 (tm-30) REVERT: B 150 MET cc_start: 0.6129 (mmm) cc_final: 0.5405 (tpt) REVERT: B 364 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 634 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7807 (m) REVERT: B 758 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7564 (t80) REVERT: B 875 TYR cc_start: 0.8494 (m-80) cc_final: 0.8248 (m-80) REVERT: B 983 PHE cc_start: 0.8839 (m-80) cc_final: 0.8518 (m-80) REVERT: B 1144 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7901 (tp40) REVERT: A 155 ARG cc_start: 0.6753 (mmp80) cc_final: 0.6439 (ttp80) REVERT: A 240 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 427 LEU cc_start: 0.6840 (mp) cc_final: 0.6279 (pt) REVERT: I 48 MET cc_start: 0.6368 (ppp) cc_final: 0.6039 (ppp) REVERT: J 87 TYR cc_start: 0.7983 (m-80) cc_final: 0.7763 (m-10) REVERT: K 37 TYR cc_start: 0.3488 (OUTLIER) cc_final: 0.2600 (t80) outliers start: 90 outliers final: 76 residues processed: 232 average time/residue: 0.3991 time to fit residues: 158.1300 Evaluate side-chains 238 residues out of total 3447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 153 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 995 ILE Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain B residue 1144 GLN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 285 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 309 optimal weight: 0.0060 chunk 129 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN B 424 ASN B 951 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.152706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.110402 restraints weight = 78582.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106504 restraints weight = 61772.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.106646 restraints weight = 57794.938| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32657 Z= 0.163 Angle : 0.581 10.924 44458 Z= 0.284 Chirality : 0.045 0.410 5165 Planarity : 0.004 0.046 5653 Dihedral : 7.599 113.458 5749 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.17 % Favored : 92.75 % Rotamer: Outliers : 2.39 % Allowed : 19.29 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3933 helix: 0.46 (0.23), residues: 610 sheet: -0.22 (0.18), residues: 865 loop : -1.91 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 36 HIS 0.003 0.001 HIS A1050 PHE 0.026 0.001 PHE C 140 TYR 0.015 0.001 TYR B1069 ARG 0.003 0.000 ARG G 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5320.45 seconds wall clock time: 99 minutes 26.17 seconds (5966.17 seconds total)