Starting phenix.real_space_refine on Fri Aug 9 10:15:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysg_34074/08_2024/7ysg_34074.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysg_34074/08_2024/7ysg_34074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysg_34074/08_2024/7ysg_34074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysg_34074/08_2024/7ysg_34074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysg_34074/08_2024/7ysg_34074.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysg_34074/08_2024/7ysg_34074.cif" } resolution = 3.18 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= 0.000 sd= 0.048 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 138 5.16 5 C 16155 2.51 5 N 4371 2.21 5 O 5012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 532": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "D TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "E GLU 532": "OE1" <-> "OE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 553": "OD1" <-> "OD2" Residue "E TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 376": "OD1" <-> "OD2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 422": "OE1" <-> "OE2" Residue "F PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 432": "OD1" <-> "OD2" Residue "F GLU 462": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 549": "OE1" <-> "OE2" Residue "F ASP 553": "OD1" <-> "OD2" Residue "F TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 443": "NH1" <-> "NH2" Residue "G GLU 468": "OE1" <-> "OE2" Residue "G TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 376": "OD1" <-> "OD2" Residue "H GLU 388": "OE1" <-> "OE2" Residue "H PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 410": "OE1" <-> "OE2" Residue "H ASP 453": "OD1" <-> "OD2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 527": "OE1" <-> "OE2" Residue "H GLU 532": "OE1" <-> "OE2" Residue "H TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 570": "OD1" <-> "OD2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J GLU 120": "OE1" <-> "OE2" Residue "J GLU 125": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 462": "OE1" <-> "OE2" Residue "K PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 498": "OE1" <-> "OE2" Residue "K ASP 553": "OD1" <-> "OD2" Residue "K TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ASP 432": "OD1" <-> "OD2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 553": "OD1" <-> "OD2" Residue "L TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 14": "OE1" <-> "OE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 99": "NH1" <-> "NH2" Residue "P ASP 104": "OD1" <-> "OD2" Residue "P GLU 108": "OE1" <-> "OE2" Residue "P PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 244": "OE1" <-> "OE2" Residue "P ASP 301": "OD1" <-> "OD2" Residue "P ASP 312": "OD1" <-> "OD2" Residue "P GLU 317": "OE1" <-> "OE2" Residue "P GLU 399": "OE1" <-> "OE2" Residue "P ASP 428": "OD1" <-> "OD2" Residue "P PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 22": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 111": "OD1" <-> "OD2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 26": "OE1" <-> "OE2" Residue "V TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25676 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1786 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1763 Classifications: {'peptide': 227} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 18, 'TRANS': 208} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "P" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3851 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 469} Chain breaks: 6 Chain: "R" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "S" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "U" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "V" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.69, per 1000 atoms: 0.53 Number of scatterers: 25676 At special positions: 0 Unit cell: (136.08, 185.76, 191.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5012 8.00 N 4371 7.00 C 16155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.23 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.04 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.51 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=1.97 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=1.98 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=1.98 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=1.98 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS K 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.06 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=1.95 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.01 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 202 " distance=2.02 Simple disulfide: pdb=" SG CYS P 239 " - pdb=" SG CYS P 307 " distance=2.02 Simple disulfide: pdb=" SG CYS P 253 " - pdb=" SG CYS P 261 " distance=2.05 Simple disulfide: pdb=" SG CYS P 353 " - pdb=" SG CYS P 423 " distance=1.95 Simple disulfide: pdb=" SG CYS P 367 " - pdb=" SG CYS P 377 " distance=2.02 Simple disulfide: pdb=" SG CYS P 464 " - pdb=" SG CYS P 526 " distance=2.06 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " distance=2.02 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 37 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 58 " distance=2.03 Simple disulfide: pdb=" SG CYS U 37 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 49 " - pdb=" SG CYS V 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 10.23 Conformation dependent library (CDL) restraints added in 4.9 seconds 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6204 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 79 sheets defined 10.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.514A pdb=" N TRP A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.674A pdb=" N LEU A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.952A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.848A pdb=" N ASN B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.828A pdb=" N SER C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.674A pdb=" N THR C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.144A pdb=" N GLY D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.983A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.602A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.785A pdb=" N TRP E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 524 through 530 removed outlier: 3.969A pdb=" N THR F 530 " --> pdb=" O GLU F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 460 through 465 Processing helix chain 'G' and resid 524 through 530 Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.574A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.540A pdb=" N CYS J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.938A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 removed outlier: 3.596A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 531 Processing helix chain 'L' and resid 353 through 361 Processing helix chain 'L' and resid 415 through 421 Processing helix chain 'L' and resid 460 through 467 removed outlier: 3.537A pdb=" N ARG L 467 " --> pdb=" O GLN L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 531 removed outlier: 3.504A pdb=" N GLY L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 557 removed outlier: 3.735A pdb=" N GLY L 557 " --> pdb=" O LYS L 554 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 33 Processing helix chain 'P' and resid 96 through 100 removed outlier: 4.170A pdb=" N GLY P 100 " --> pdb=" O ASN P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 247 removed outlier: 3.880A pdb=" N ASN P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 272 through 276 removed outlier: 4.034A pdb=" N GLU P 276 " --> pdb=" O PRO P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 302 removed outlier: 3.727A pdb=" N ALA P 302 " --> pdb=" O LYS P 299 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'V' and resid 69 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.722A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 372 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 383 removed outlier: 7.060A pdb=" N TRP A 382 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 424 through 427 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.611A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA7, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.504A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR J 62 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 349 Processing sheet with id=AA9, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB1, first strand: chain 'B' and resid 425 through 428 removed outlier: 3.584A pdb=" N GLN B 439 " --> pdb=" O CYS B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AB3, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AB4, first strand: chain 'B' and resid 485 through 489 Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.562A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS C 364 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 413 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR C 366 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA C 411 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU C 368 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 409 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 372 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.541A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.725A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 455 through 457 removed outlier: 5.560A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.553A pdb=" N GLN C 490 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.850A pdb=" N THR D 363 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 411 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 378 through 379 removed outlier: 3.831A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 378 through 379 Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.746A pdb=" N GLY D 478 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.746A pdb=" N GLY D 478 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.857A pdb=" N GLN D 493 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN D 490 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 562 through 567 removed outlier: 6.826A pdb=" N TYR D 562 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER E 565 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 564 " --> pdb=" O SER E 565 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL E 567 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.669A pdb=" N ALA E 411 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 424 through 428 Processing sheet with id=AD1, first strand: chain 'E' and resid 453 through 457 Processing sheet with id=AD2, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AD3, first strand: chain 'F' and resid 382 through 384 Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.045A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 520 " --> pdb=" O VAL F 501 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.550A pdb=" N CYS F 536 " --> pdb=" O ARG F 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.836A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 380 through 384 Processing sheet with id=AD8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.826A pdb=" N LEU G 457 " --> pdb=" O THR G 473 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 517 " --> pdb=" O VAL G 476 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.826A pdb=" N LEU G 457 " --> pdb=" O THR G 473 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE2, first strand: chain 'H' and resid 347 through 348 Processing sheet with id=AE3, first strand: chain 'H' and resid 381 through 382 removed outlier: 3.558A pdb=" N SER H 381 " --> pdb=" O THR H 427 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR H 427 " --> pdb=" O SER H 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 453 through 457 Processing sheet with id=AE5, first strand: chain 'H' and resid 453 through 457 removed outlier: 5.303A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.562A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 5 through 10 removed outlier: 5.414A pdb=" N VAL J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER J 19 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 18 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AE9, first strand: chain 'J' and resid 103 through 104 removed outlier: 6.607A pdb=" N TYR J 103 " --> pdb=" O CYS L 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 110 through 114 Processing sheet with id=AF2, first strand: chain 'K' and resid 346 through 347 removed outlier: 3.779A pdb=" N ARG K 346 " --> pdb=" O THR K 370 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 363 through 364 removed outlier: 3.930A pdb=" N ILE K 413 " --> pdb=" O THR K 363 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 380 through 383 removed outlier: 3.666A pdb=" N SER K 381 " --> pdb=" O THR K 427 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 454 through 457 Processing sheet with id=AF6, first strand: chain 'K' and resid 454 through 457 Processing sheet with id=AF7, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.565A pdb=" N GLN K 493 " --> pdb=" O GLN K 490 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 561 through 562 removed outlier: 6.830A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'L' and resid 349 through 350 removed outlier: 4.277A pdb=" N ILE L 350 " --> pdb=" O THR L 366 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AG2, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AG3, first strand: chain 'L' and resid 493 through 494 removed outlier: 3.642A pdb=" N MET L 489 " --> pdb=" O THR L 535 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 11 through 13 removed outlier: 6.486A pdb=" N SER P 12 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG P 39 " --> pdb=" O THR P 48 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR P 48 " --> pdb=" O ARG P 39 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY P 41 " --> pdb=" O CYS P 46 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS P 46 " --> pdb=" O GLY P 41 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AG6, first strand: chain 'P' and resid 121 through 125 removed outlier: 3.530A pdb=" N LEU P 220 " --> pdb=" O VAL P 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 130 through 133 Processing sheet with id=AG8, first strand: chain 'P' and resid 202 through 203 Processing sheet with id=AG9, first strand: chain 'P' and resid 225 through 230 removed outlier: 6.684A pdb=" N GLU P 225 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE P 327 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 234 through 240 removed outlier: 4.051A pdb=" N PHE P 290 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 251 through 252 removed outlier: 3.775A pdb=" N VAL P 265 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 343 through 344 removed outlier: 5.706A pdb=" N GLY P 343 " --> pdb=" O ILE P 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'P' and resid 351 through 352 Processing sheet with id=AH5, first strand: chain 'P' and resid 419 through 422 Processing sheet with id=AH6, first strand: chain 'P' and resid 463 through 464 removed outlier: 3.854A pdb=" N CYS P 464 " --> pdb=" O ARG P 507 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 486 through 487 removed outlier: 3.561A pdb=" N GLN P 486 " --> pdb=" O LYS P 479 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 22 through 24 removed outlier: 5.479A pdb=" N VAL R 23 " --> pdb=" O THR R 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'R' and resid 34 through 38 Processing sheet with id=AI1, first strand: chain 'R' and resid 58 through 62 removed outlier: 5.274A pdb=" N THR R 60 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG R 50 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 62 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 33 through 38 Processing sheet with id=AI3, first strand: chain 'S' and resid 58 through 63 removed outlier: 6.589A pdb=" N LEU S 48 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER S 63 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE S 46 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA S 106 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS S 114 " --> pdb=" O ALA S 106 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 33 through 38 Processing sheet with id=AI5, first strand: chain 'U' and resid 58 through 63 removed outlier: 6.700A pdb=" N LEU U 48 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER U 63 " --> pdb=" O ILE U 46 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE U 46 " --> pdb=" O SER U 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY U 105 " --> pdb=" O TYR U 47 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR U 102 " --> pdb=" O LYS U 117 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS U 117 " --> pdb=" O TYR U 102 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS U 104 " --> pdb=" O THR U 115 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AI7, first strand: chain 'V' and resid 60 through 62 removed outlier: 5.095A pdb=" N THR V 60 " --> pdb=" O ARG V 50 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG V 50 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL V 62 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR V 102 " --> pdb=" O LYS V 117 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS V 117 " --> pdb=" O TYR V 102 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS V 104 " --> pdb=" O THR V 115 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1749 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: 9.44 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4210 1.26 - 1.40: 6218 1.40 - 1.55: 15572 1.55 - 1.69: 87 1.69 - 1.83: 180 Bond restraints: 26267 Sorted by residual: bond pdb=" C GLY P 404 " pdb=" N THR P 405 " ideal model delta sigma weight residual 1.332 1.523 -0.190 1.40e-02 5.10e+03 1.85e+02 bond pdb=" C CYS H 536 " pdb=" O CYS H 536 " ideal model delta sigma weight residual 1.235 1.123 0.112 1.13e-02 7.83e+03 9.90e+01 bond pdb=" C VAL L 567 " pdb=" O VAL L 567 " ideal model delta sigma weight residual 1.238 1.134 0.104 1.06e-02 8.90e+03 9.54e+01 bond pdb=" C TYR G 562 " pdb=" O TYR G 562 " ideal model delta sigma weight residual 1.234 1.127 0.108 1.11e-02 8.12e+03 9.45e+01 bond pdb=" CA THR B 477 " pdb=" C THR B 477 " ideal model delta sigma weight residual 1.520 1.404 0.116 1.20e-02 6.94e+03 9.41e+01 ... (remaining 26262 not shown) Histogram of bond angle deviations from ideal: 93.46 - 104.86: 945 104.86 - 116.27: 17527 116.27 - 127.67: 17023 127.67 - 139.07: 343 139.07 - 150.47: 3 Bond angle restraints: 35841 Sorted by residual: angle pdb=" C GLN E 493 " pdb=" N PRO E 494 " pdb=" CA PRO E 494 " ideal model delta sigma weight residual 119.84 142.99 -23.15 1.25e+00 6.40e-01 3.43e+02 angle pdb=" N THR L 551 " pdb=" CA THR L 551 " pdb=" C THR L 551 " ideal model delta sigma weight residual 109.40 136.17 -26.77 1.63e+00 3.76e-01 2.70e+02 angle pdb=" C GLY P 404 " pdb=" N THR P 405 " pdb=" CA THR P 405 " ideal model delta sigma weight residual 121.54 149.50 -27.96 1.91e+00 2.74e-01 2.14e+02 angle pdb=" C SER B 496 " pdb=" N PRO B 497 " pdb=" CA PRO B 497 " ideal model delta sigma weight residual 119.84 137.59 -17.75 1.25e+00 6.40e-01 2.02e+02 angle pdb=" N VAL L 552 " pdb=" CA VAL L 552 " pdb=" C VAL L 552 " ideal model delta sigma weight residual 108.06 125.56 -17.50 1.28e+00 6.10e-01 1.87e+02 ... (remaining 35836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.59: 14780 26.59 - 53.19: 1109 53.19 - 79.78: 203 79.78 - 106.38: 21 106.38 - 132.97: 10 Dihedral angle restraints: 16123 sinusoidal: 6544 harmonic: 9579 Sorted by residual: dihedral pdb=" CA SER C 480 " pdb=" C SER C 480 " pdb=" N PRO C 481 " pdb=" CA PRO C 481 " ideal model delta harmonic sigma weight residual -180.00 -75.27 -104.73 0 5.00e+00 4.00e-02 4.39e+02 dihedral pdb=" C THR L 551 " pdb=" N THR L 551 " pdb=" CA THR L 551 " pdb=" CB THR L 551 " ideal model delta harmonic sigma weight residual -122.00 -151.42 29.42 0 2.50e+00 1.60e-01 1.39e+02 dihedral pdb=" N GLU C 525 " pdb=" C GLU C 525 " pdb=" CA GLU C 525 " pdb=" CB GLU C 525 " ideal model delta harmonic sigma weight residual 122.80 151.03 -28.23 0 2.50e+00 1.60e-01 1.28e+02 ... (remaining 16120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 4071 0.285 - 0.570: 113 0.570 - 0.855: 17 0.855 - 1.140: 1 1.140 - 1.425: 3 Chirality restraints: 4205 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN J 48 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.98 -1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" CA THR L 551 " pdb=" N THR L 551 " pdb=" C THR L 551 " pdb=" CB THR L 551 " both_signs ideal model delta sigma weight residual False 2.53 1.10 1.42 2.00e-01 2.50e+01 5.05e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.80e+01 ... (remaining 4202 not shown) Planarity restraints: 4587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.425 2.00e-02 2.50e+03 3.48e-01 1.51e+03 pdb=" C7 NAG I 2 " -0.128 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.211 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.596 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 601 " 0.358 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG H 601 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 601 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG H 601 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG H 601 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 601 " -0.343 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG G 601 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG G 601 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG G 601 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG G 601 " -0.070 2.00e-02 2.50e+03 ... (remaining 4584 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 47 1.93 - 2.67: 1981 2.67 - 3.42: 35352 3.42 - 4.16: 61860 4.16 - 4.90: 109196 Nonbonded interactions: 208436 Sorted by model distance: nonbonded pdb=" SG CYS P 261 " pdb=" CD2 LEU P 315 " model vdw 1.189 3.820 nonbonded pdb=" O VAL P 344 " pdb=" CD1 LEU P 413 " model vdw 1.253 3.460 nonbonded pdb=" OE2 GLU A 549 " pdb=" CG2 THR J 126 " model vdw 1.258 3.460 nonbonded pdb=" N HIS F 450 " pdb=" OG SER F 480 " model vdw 1.305 3.120 nonbonded pdb=" OE2 GLU A 525 " pdb=" ND2 ASN A 529 " model vdw 1.368 3.120 ... (remaining 208431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 568 or resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'G' and (resid 345 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or (resid 601 and (name C1 or name C2 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 o \ r name O4 or name O5 or name O6 or name O7 )))) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } ncs_group { reference = (chain 'R' and resid 20 through 119) selection = (chain 'S' and resid 20 through 119) selection = (chain 'U' and resid 20 through 119) selection = (chain 'V' and resid 20 through 119) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 67.070 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.017 0.190 26267 Z= 1.095 Angle : 1.732 27.961 35841 Z= 1.047 Chirality : 0.113 1.425 4205 Planarity : 0.013 0.348 4578 Dihedral : 18.112 132.971 9793 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 44.73 Ramachandran Plot: Outliers : 3.27 % Allowed : 9.90 % Favored : 86.84 % Rotamer: Outliers : 11.57 % Allowed : 5.82 % Favored : 82.60 % Cbeta Deviations : 2.77 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3244 helix: -1.22 (0.30), residues: 258 sheet: -0.76 (0.16), residues: 1052 loop : -2.10 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP P 480 HIS 0.024 0.002 HIS B 450 PHE 0.069 0.003 PHE P 275 TYR 0.041 0.003 TYR K 576 ARG 0.029 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 404 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: A 543 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9069 (mp) REVERT: B 375 TYR cc_start: 0.3261 (OUTLIER) cc_final: 0.2213 (m-80) REVERT: B 418 TRP cc_start: 0.6135 (t60) cc_final: 0.5836 (t60) REVERT: C 386 ASN cc_start: 0.8138 (t0) cc_final: 0.7921 (t0) REVERT: C 526 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: D 424 PHE cc_start: 0.7553 (m-80) cc_final: 0.7297 (m-80) REVERT: E 445 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6921 (mmtp) REVERT: F 364 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7757 (mtpp) REVERT: F 376 ASP cc_start: 0.2528 (OUTLIER) cc_final: 0.2288 (t0) REVERT: F 414 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5853 (m) REVERT: F 416 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7405 (p0) REVERT: F 554 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (tmtm) REVERT: G 417 ASP cc_start: 0.7050 (m-30) cc_final: 0.6729 (m-30) REVERT: G 445 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.6581 (mmpt) REVERT: J 35 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8147 (ttm170) REVERT: K 368 LEU cc_start: 0.6466 (pt) cc_final: 0.5566 (tt) REVERT: K 391 LYS cc_start: 0.7488 (tptt) cc_final: 0.6883 (tptm) REVERT: K 490 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7291 (tp40) REVERT: L 453 ASP cc_start: 0.8095 (t0) cc_final: 0.7818 (t0) REVERT: L 479 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: P 99 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8351 (tpt90) REVERT: P 358 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (tptt) REVERT: P 390 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6473 (tp40) REVERT: P 392 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: P 400 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: P 432 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7998 (mpt180) REVERT: P 447 LYS cc_start: 0.4111 (OUTLIER) cc_final: 0.3549 (tptt) REVERT: P 469 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6381 (pptt) REVERT: P 533 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: P 541 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: S 71 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: S 73 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7805 (mtpt) REVERT: U 44 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8044 (t) REVERT: U 83 ARG cc_start: 0.8399 (mpp80) cc_final: 0.8156 (ptt90) REVERT: U 88 LEU cc_start: 0.7230 (mt) cc_final: 0.6953 (mt) REVERT: U 112 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7529 (ttp80) REVERT: U 117 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.4897 (mttt) outliers start: 336 outliers final: 182 residues processed: 696 average time/residue: 0.4061 time to fit residues: 430.9047 Evaluate side-chains 540 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 331 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 479 PHE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 544 PRO Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 554 LYS Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 516 PHE Chi-restraints excluded: chain H residue 442 SER Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain H residue 444 PRO Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 519 SER Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain H residue 568 MET Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 565 SER Chi-restraints excluded: chain K residue 568 MET Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 479 PHE Chi-restraints excluded: chain L residue 480 SER Chi-restraints excluded: chain L residue 534 TYR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 556 THR Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 245 VAL Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 259 GLU Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 290 PHE Chi-restraints excluded: chain P residue 314 GLN Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 317 GLU Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 349 VAL Chi-restraints excluded: chain P residue 358 LYS Chi-restraints excluded: chain P residue 361 LYS Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 GLN Chi-restraints excluded: chain P residue 392 GLU Chi-restraints excluded: chain P residue 398 LEU Chi-restraints excluded: chain P residue 400 GLU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 432 ARG Chi-restraints excluded: chain P residue 439 ILE Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 470 PHE Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 478 CYS Chi-restraints excluded: chain P residue 533 PHE Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 541 TYR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 72 TYR Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 GLN Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 117 LYS Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 114 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 135 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: