Starting phenix.real_space_refine on Tue Feb 20 08:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7b_30998/02_2024/7e7b_30998_updated.pdb" } resolution = 2.6 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17370 2.51 5 N 4413 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27363 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8613 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 51, 'TRANS': 1050} Chain breaks: 3 Chain: "B" Number of atoms: 8613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8613 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 51, 'TRANS': 1050} Chain breaks: 3 Chain: "C" Number of atoms: 8613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8613 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 51, 'TRANS': 1050} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "L" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Unusual residues: {'ELA': 2, 'NAG': 5, 'VCG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Unusual residues: {'ELA': 1, 'NAG': 5, 'VCG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 13.77, per 1000 atoms: 0.50 Number of scatterers: 27363 At special positions: 0 Unit cell: (146.745, 151.093, 177.181, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5460 8.00 N 4413 7.00 C 17370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A1601 " - " ASN A 343 " " NAG A1602 " - " ASN A 331 " " NAG A1603 " - " ASN A 603 " " NAG A1604 " - " ASN A 657 " " NAG A1605 " - " ASN A 61 " " NAG B1601 " - " ASN B 343 " " NAG B1602 " - " ASN B 331 " " NAG B1603 " - " ASN B 603 " " NAG B1604 " - " ASN B 657 " " NAG B1605 " - " ASN B 61 " " NAG C1601 " - " ASN C 343 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 603 " " NAG C1604 " - " ASN C 657 " " NAG C1605 " - " ASN C 61 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 149 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN A 17 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B 282 " " NAG V 1 " - " ASN B 234 " " NAG W 1 " - " ASN B 122 " " NAG X 1 " - " ASN B 149 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 165 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B 17 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " " NAG h 1 " - " ASN C 282 " " NAG i 1 " - " ASN C 234 " " NAG j 1 " - " ASN C 122 " " NAG k 1 " - " ASN C 149 " " NAG l 1 " - " ASN C 801 " " NAG m 1 " - " ASN C 709 " " NAG n 1 " - " ASN C 165 " " NAG o 1 " - " ASN C1074 " " NAG p 1 " - " ASN C 17 " Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 4.5 seconds 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 41 sheets defined 21.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.40 Creating SS restraints... Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.830A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.512A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.797A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 844 through 847 No H-bonds generated for 'chain 'A' and resid 844 through 847' Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.580A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.986A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.049A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.832A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.512A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 782 removed outlier: 4.798A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 844 through 847 No H-bonds generated for 'chain 'B' and resid 844 through 847' Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.555A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 887 through 890 No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.986A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.049A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 No H-bonds generated for 'chain 'B' and resid 1142 through 1145' Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.833A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.511A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 782 removed outlier: 4.797A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 844 through 847 No H-bonds generated for 'chain 'C' and resid 844 through 847' Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.555A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.986A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.049A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 No H-bonds generated for 'chain 'C' and resid 1142 through 1145' Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.979A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 56 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.574A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 242 through 246 removed outlier: 5.918A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.673A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.199A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.115A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.217A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.528A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.906A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.445A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.980A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.854A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.575A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 242 through 246 removed outlier: 5.919A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.674A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.212A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.137A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.216A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.528A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 717 through 728 removed outlier: 5.905A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.356A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AB, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.980A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 47 through 56 removed outlier: 3.853A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.574A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 242 through 246 removed outlier: 5.919A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.672A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.212A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AI, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AJ, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.148A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.217A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.529A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.906A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.355A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 1088 through 1090 973 hydrogen bonds defined for protein. 2712 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: 11.27 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4478 1.32 - 1.45: 8522 1.45 - 1.58: 14764 1.58 - 1.72: 7 1.72 - 1.85: 150 Bond restraints: 27921 Sorted by residual: bond pdb=" C29 VCG A1609 " pdb=" O30 VCG A1609 " ideal model delta sigma weight residual 1.544 1.281 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C29 VCG A1608 " pdb=" O30 VCG A1608 " ideal model delta sigma weight residual 1.544 1.281 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C29 VCG B1607 " pdb=" O30 VCG B1607 " ideal model delta sigma weight residual 1.544 1.282 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C26 VCG B1607 " pdb=" O30 VCG B1607 " ideal model delta sigma weight residual 1.262 1.466 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C26 VCG A1608 " pdb=" O30 VCG A1608 " ideal model delta sigma weight residual 1.262 1.466 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 27916 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.16: 485 105.16 - 112.40: 14738 112.40 - 119.63: 8739 119.63 - 126.86: 13694 126.86 - 134.10: 279 Bond angle restraints: 37935 Sorted by residual: angle pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 111.36 129.43 -18.07 1.09e+00 8.42e-01 2.75e+02 angle pdb=" N ASN A 149 " pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 114.04 99.53 14.51 1.24e+00 6.50e-01 1.37e+02 angle pdb=" C08 VCG A1608 " pdb=" C09 VCG A1608 " pdb=" C10 VCG A1608 " ideal model delta sigma weight residual 152.67 119.74 32.93 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C08 VCG A1609 " pdb=" C09 VCG A1609 " pdb=" C10 VCG A1609 " ideal model delta sigma weight residual 152.67 120.13 32.54 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C08 VCG B1607 " pdb=" C09 VCG B1607 " pdb=" C10 VCG B1607 " ideal model delta sigma weight residual 152.67 120.63 32.04 3.00e+00 1.11e-01 1.14e+02 ... (remaining 37930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 16920 27.04 - 54.08: 809 54.08 - 81.12: 96 81.12 - 108.16: 15 108.16 - 135.20: 4 Dihedral angle restraints: 17844 sinusoidal: 8223 harmonic: 9621 Sorted by residual: dihedral pdb=" C THR A 393 " pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" CB THR A 393 " ideal model delta harmonic sigma weight residual -122.00 -146.69 24.69 0 2.50e+00 1.60e-01 9.75e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.77 74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.76 74.76 1 1.00e+01 1.00e-02 7.08e+01 ... (remaining 17841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 4479 0.194 - 0.388: 58 0.388 - 0.582: 4 0.582 - 0.776: 0 0.776 - 0.970: 1 Chirality restraints: 4542 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.03e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 9.86e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.19e+01 ... (remaining 4539 not shown) Planarity restraints: 4830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1601 " -0.360 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG B1601 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B1601 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG B1601 " 0.550 2.00e-02 2.50e+03 pdb=" O7 NAG B1601 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1601 " -0.359 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG C1601 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG C1601 " -0.130 2.00e-02 2.50e+03 pdb=" N2 NAG C1601 " 0.548 2.00e-02 2.50e+03 pdb=" O7 NAG C1601 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1601 " 0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG A1601 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1601 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1601 " 0.085 2.00e-02 2.50e+03 ... (remaining 4827 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3441 2.74 - 3.28: 24980 3.28 - 3.82: 46022 3.82 - 4.36: 57874 4.36 - 4.90: 97393 Nonbonded interactions: 229710 Sorted by model distance: nonbonded pdb=" OG1 THR C 76 " pdb=" O TRP C 258 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR A 76 " pdb=" O TRP A 258 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR B 76 " pdb=" O TRP B 258 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP A 843 " pdb=" NH1 ARG A 847 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP C 843 " pdb=" NH1 ARG C 847 " model vdw 2.201 2.520 ... (remaining 229705 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' and (resid 14 through 1147 or resid 1601 through 1605)) selection = (chain 'B' and (resid 14 through 1147 or resid 1601 through 1605)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 1.390 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: 6.050 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 73.170 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.540 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.011 0.263 27921 Z= 0.672 Angle : 0.954 32.933 37935 Z= 0.527 Chirality : 0.066 0.970 4542 Planarity : 0.020 0.310 4776 Dihedral : 14.730 135.197 11529 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.49 % Allowed : 4.07 % Favored : 90.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 3282 helix: -1.24 (0.16), residues: 747 sheet: -0.22 (0.18), residues: 744 loop : -1.91 (0.12), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.004 0.001 HIS B1101 PHE 0.016 0.002 PHE A 133 TYR 0.018 0.002 TYR A 495 ARG 0.003 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 289 time to evaluate : 3.005 Fit side-chains REVERT: A 14 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6858 (mp-120) REVERT: A 935 GLN cc_start: 0.8661 (tt0) cc_final: 0.8377 (tt0) REVERT: A 1029 MET cc_start: 0.8827 (tpp) cc_final: 0.8548 (tpp) REVERT: A 1138 TYR cc_start: 0.8461 (t80) cc_final: 0.8223 (t80) REVERT: A 1142 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7121 (tp40) REVERT: B 155 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8519 (p) REVERT: B 179 LEU cc_start: 0.8861 (mt) cc_final: 0.8645 (mt) REVERT: B 346 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7657 (mtp-110) REVERT: B 583 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: B 697 MET cc_start: 0.8718 (ptm) cc_final: 0.8329 (ptm) REVERT: B 935 GLN cc_start: 0.8676 (tt0) cc_final: 0.8439 (tt0) REVERT: C 14 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6881 (mp-120) REVERT: C 900 MET cc_start: 0.8788 (mtp) cc_final: 0.8530 (mtt) outliers start: 158 outliers final: 18 residues processed: 406 average time/residue: 1.2295 time to fit residues: 591.1274 Evaluate side-chains 170 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 299 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 69 HIS A 115 GLN A 134 GLN A 314 GLN A 317 ASN A 474 GLN A 487 ASN A 607 GLN A 779 GLN A 901 GLN A 926 GLN A1119 ASN B 30 ASN B 69 HIS B 115 GLN B 314 GLN B 317 ASN B 474 GLN B 607 GLN B 675 GLN B 779 GLN B 901 GLN B 926 GLN B1002 GLN B1119 ASN C 30 ASN C 115 GLN C 317 ASN C 474 GLN C 487 ASN C 493 GLN C 607 GLN C 779 GLN C 901 GLN C 926 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27921 Z= 0.225 Angle : 0.586 9.100 37935 Z= 0.300 Chirality : 0.045 0.401 4542 Planarity : 0.003 0.029 4776 Dihedral : 10.199 129.945 5670 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.54 % Allowed : 9.77 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3282 helix: 0.16 (0.18), residues: 750 sheet: 0.02 (0.18), residues: 786 loop : -1.61 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B 146 PHE 0.012 0.001 PHE A 392 TYR 0.015 0.001 TYR A1067 ARG 0.003 0.000 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 3.122 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: A 935 GLN cc_start: 0.8647 (tt0) cc_final: 0.8369 (tt0) REVERT: A 1138 TYR cc_start: 0.8350 (t80) cc_final: 0.8136 (t80) REVERT: B 583 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 697 MET cc_start: 0.8673 (ptm) cc_final: 0.8404 (ptm) REVERT: B 808 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6100 (m-30) REVERT: B 935 GLN cc_start: 0.8631 (tt0) cc_final: 0.8398 (tt0) REVERT: B 1038 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8137 (mmtp) REVERT: C 164 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6880 (p0) REVERT: C 528 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8447 (tttm) REVERT: C 900 MET cc_start: 0.8697 (mtp) cc_final: 0.8470 (mtt) outliers start: 73 outliers final: 32 residues processed: 233 average time/residue: 1.2675 time to fit residues: 349.3103 Evaluate side-chains 191 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN A 804 GLN B 69 HIS B 493 GLN B 804 GLN B1002 GLN C 69 HIS C 134 GLN C 314 GLN C 675 GLN C 764 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27921 Z= 0.247 Angle : 0.545 6.591 37935 Z= 0.280 Chirality : 0.044 0.184 4542 Planarity : 0.003 0.031 4776 Dihedral : 8.992 121.849 5645 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 10.50 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3282 helix: 0.77 (0.19), residues: 732 sheet: 0.23 (0.18), residues: 771 loop : -1.37 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS B 69 PHE 0.015 0.001 PHE A 392 TYR 0.018 0.001 TYR C1138 ARG 0.006 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 177 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: A 804 GLN cc_start: 0.8267 (mm110) cc_final: 0.7971 (mp10) REVERT: A 935 GLN cc_start: 0.8634 (tt0) cc_final: 0.8394 (tt0) REVERT: B 21 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7704 (mtm180) REVERT: B 583 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: B 697 MET cc_start: 0.8611 (ptm) cc_final: 0.8348 (ptm) REVERT: B 808 ASP cc_start: 0.6532 (OUTLIER) cc_final: 0.6078 (m-30) REVERT: B 916 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 1038 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8141 (mmtp) REVERT: C 153 MET cc_start: 0.7678 (mtp) cc_final: 0.7455 (mtt) REVERT: C 211 ASN cc_start: 0.8706 (t0) cc_final: 0.8421 (t0) REVERT: C 516 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: C 528 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8561 (tttm) REVERT: C 900 MET cc_start: 0.8720 (mtp) cc_final: 0.8455 (mtt) outliers start: 73 outliers final: 34 residues processed: 224 average time/residue: 1.2790 time to fit residues: 340.2592 Evaluate side-chains 199 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 285 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN B 69 HIS B1002 GLN B1010 GLN C 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27921 Z= 0.235 Angle : 0.524 6.871 37935 Z= 0.270 Chirality : 0.043 0.175 4542 Planarity : 0.003 0.048 4776 Dihedral : 8.394 115.389 5640 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.75 % Allowed : 11.05 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3282 helix: 1.20 (0.20), residues: 693 sheet: 0.27 (0.18), residues: 780 loop : -1.26 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.003 0.001 HIS C 69 PHE 0.012 0.001 PHE A 133 TYR 0.018 0.001 TYR C1138 ARG 0.015 0.000 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 179 time to evaluate : 3.125 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7419 (p-80) REVERT: A 804 GLN cc_start: 0.8243 (mm110) cc_final: 0.7950 (mp10) REVERT: A 935 GLN cc_start: 0.8628 (tt0) cc_final: 0.8415 (tt0) REVERT: A 1029 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8514 (tpp) REVERT: B 21 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7590 (mtm180) REVERT: B 493 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 697 MET cc_start: 0.8581 (ptm) cc_final: 0.8283 (ptm) REVERT: B 808 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.5982 (m-30) REVERT: B 916 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 1038 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8111 (mmtp) REVERT: C 211 ASN cc_start: 0.8639 (t0) cc_final: 0.8403 (t0) REVERT: C 528 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8606 (tttm) REVERT: C 900 MET cc_start: 0.8711 (mtp) cc_final: 0.8435 (mtt) outliers start: 79 outliers final: 37 residues processed: 233 average time/residue: 1.2059 time to fit residues: 335.9005 Evaluate side-chains 205 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 0.2980 chunk 181 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 675 GLN B1002 GLN C 69 HIS C 675 GLN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27921 Z= 0.231 Angle : 0.525 9.408 37935 Z= 0.268 Chirality : 0.043 0.172 4542 Planarity : 0.003 0.051 4776 Dihedral : 8.153 114.105 5637 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.57 % Allowed : 11.51 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3282 helix: 1.28 (0.20), residues: 693 sheet: 0.28 (0.18), residues: 783 loop : -1.20 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 152 HIS 0.002 0.001 HIS C1101 PHE 0.012 0.001 PHE C 133 TYR 0.017 0.001 TYR C1138 ARG 0.013 0.000 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 175 time to evaluate : 3.203 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7286 (p-80) REVERT: A 169 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 935 GLN cc_start: 0.8625 (tt0) cc_final: 0.8353 (tt0) REVERT: A 1029 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8533 (tpp) REVERT: B 21 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7702 (mtm180) REVERT: B 271 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: B 493 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: B 697 MET cc_start: 0.8554 (ptm) cc_final: 0.8254 (ptm) REVERT: B 808 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.5864 (m-30) REVERT: B 916 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (tt) REVERT: B 1038 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8122 (mmtp) REVERT: C 211 ASN cc_start: 0.8610 (t0) cc_final: 0.8392 (t0) REVERT: C 528 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8610 (tttm) REVERT: C 804 GLN cc_start: 0.8339 (mm110) cc_final: 0.8096 (mp10) REVERT: C 900 MET cc_start: 0.8705 (mtp) cc_final: 0.8431 (mtt) REVERT: C 916 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8489 (tt) REVERT: C 1005 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8006 (tp40) outliers start: 74 outliers final: 44 residues processed: 224 average time/residue: 1.2634 time to fit residues: 338.9205 Evaluate side-chains 221 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 69 HIS B 498 GLN B 675 GLN B1002 GLN C 519 HIS C 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27921 Z= 0.390 Angle : 0.596 8.547 37935 Z= 0.305 Chirality : 0.046 0.183 4542 Planarity : 0.004 0.054 4776 Dihedral : 8.397 119.351 5637 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.92 % Allowed : 11.85 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3282 helix: 1.06 (0.20), residues: 693 sheet: 0.26 (0.18), residues: 762 loop : -1.23 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 152 HIS 0.004 0.001 HIS C1101 PHE 0.017 0.002 PHE C 133 TYR 0.021 0.002 TYR A 904 ARG 0.015 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 171 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7440 (p-80) REVERT: A 169 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: A 804 GLN cc_start: 0.8161 (mm110) cc_final: 0.7922 (mp10) REVERT: A 1029 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8552 (tpp) REVERT: B 21 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7756 (mtm180) REVERT: B 271 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: B 493 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: B 697 MET cc_start: 0.8569 (ptm) cc_final: 0.8287 (ptm) REVERT: B 808 ASP cc_start: 0.6285 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: B 916 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (tt) REVERT: B 1038 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8143 (mmtp) REVERT: C 118 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8815 (tp) REVERT: C 271 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: C 804 GLN cc_start: 0.8365 (mm110) cc_final: 0.8136 (mp10) REVERT: C 900 MET cc_start: 0.8713 (mtp) cc_final: 0.8436 (mtt) REVERT: C 916 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8589 (tt) outliers start: 84 outliers final: 48 residues processed: 230 average time/residue: 1.2777 time to fit residues: 350.2160 Evaluate side-chains 221 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 161 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 675 GLN B1002 GLN C 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27921 Z= 0.212 Angle : 0.518 8.540 37935 Z= 0.265 Chirality : 0.043 0.179 4542 Planarity : 0.003 0.062 4776 Dihedral : 7.964 114.457 5637 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 12.23 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3282 helix: 1.32 (0.20), residues: 693 sheet: 0.36 (0.18), residues: 753 loop : -1.16 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 152 HIS 0.002 0.001 HIS C1101 PHE 0.011 0.001 PHE C 133 TYR 0.021 0.001 TYR A 904 ARG 0.017 0.000 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 178 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7274 (p-80) REVERT: A 169 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: A 935 GLN cc_start: 0.8608 (tt0) cc_final: 0.8332 (tt0) REVERT: A 1029 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8538 (tpp) REVERT: B 21 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7718 (mtm180) REVERT: B 271 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: B 697 MET cc_start: 0.8573 (ptm) cc_final: 0.8130 (ptm) REVERT: B 916 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8493 (tt) REVERT: B 1038 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8122 (mmtp) REVERT: C 271 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: C 804 GLN cc_start: 0.8351 (mm110) cc_final: 0.8093 (mp10) REVERT: C 900 MET cc_start: 0.8697 (mtp) cc_final: 0.8436 (mtt) REVERT: C 916 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8478 (tt) REVERT: C 1005 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7975 (tp40) outliers start: 73 outliers final: 43 residues processed: 224 average time/residue: 1.2639 time to fit residues: 336.3009 Evaluate side-chains 221 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 157 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 675 GLN B1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27921 Z= 0.254 Angle : 0.533 8.187 37935 Z= 0.274 Chirality : 0.043 0.167 4542 Planarity : 0.004 0.072 4776 Dihedral : 7.915 114.307 5637 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.40 % Allowed : 12.58 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3282 helix: 1.33 (0.20), residues: 693 sheet: 0.36 (0.18), residues: 753 loop : -1.14 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 152 HIS 0.002 0.001 HIS C1101 PHE 0.013 0.001 PHE A 133 TYR 0.024 0.001 TYR A 904 ARG 0.018 0.001 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 175 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7312 (p-80) REVERT: A 169 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 935 GLN cc_start: 0.8609 (tt0) cc_final: 0.8329 (tt0) REVERT: A 1029 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8543 (tpp) REVERT: B 21 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7841 (mtm180) REVERT: B 271 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: B 697 MET cc_start: 0.8564 (ptm) cc_final: 0.8119 (ptm) REVERT: B 916 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8516 (tt) REVERT: B 1038 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8132 (mmtp) REVERT: C 271 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: C 804 GLN cc_start: 0.8361 (mm110) cc_final: 0.8094 (mp10) REVERT: C 900 MET cc_start: 0.8666 (mtp) cc_final: 0.8395 (mtt) REVERT: C 916 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8499 (tt) REVERT: C 1005 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8022 (tp40) outliers start: 69 outliers final: 45 residues processed: 222 average time/residue: 1.2914 time to fit residues: 345.9407 Evaluate side-chains 222 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 168 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 278 optimal weight: 0.0770 chunk 296 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 267 optimal weight: 0.5980 chunk 280 optimal weight: 5.9990 chunk 295 optimal weight: 0.0060 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN B 69 HIS B 675 GLN B1002 GLN C 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27921 Z= 0.140 Angle : 0.481 8.061 37935 Z= 0.247 Chirality : 0.042 0.181 4542 Planarity : 0.003 0.074 4776 Dihedral : 7.393 106.705 5637 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.67 % Allowed : 13.28 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3282 helix: 1.84 (0.20), residues: 669 sheet: 0.32 (0.18), residues: 765 loop : -1.05 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 152 HIS 0.003 0.000 HIS B 146 PHE 0.009 0.001 PHE A 133 TYR 0.031 0.001 TYR B 904 ARG 0.018 0.000 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.8609 (tt0) cc_final: 0.8353 (tt0) REVERT: A 1029 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8486 (tpp) REVERT: B 21 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7793 (mtm180) REVERT: B 271 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: B 697 MET cc_start: 0.8537 (ptm) cc_final: 0.8222 (ptm) REVERT: C 144 TYR cc_start: 0.9000 (t80) cc_final: 0.8742 (t80) REVERT: C 176 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 271 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: C 900 MET cc_start: 0.8630 (mtp) cc_final: 0.8397 (mtt) REVERT: C 1005 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7957 (tp40) outliers start: 48 outliers final: 30 residues processed: 225 average time/residue: 1.2920 time to fit residues: 347.7528 Evaluate side-chains 213 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 328 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A1002 GLN B 69 HIS B 675 GLN B1002 GLN C 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 27921 Z= 0.389 Angle : 0.588 8.996 37935 Z= 0.302 Chirality : 0.046 0.164 4542 Planarity : 0.004 0.064 4776 Dihedral : 7.912 113.929 5637 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.49 % Allowed : 14.08 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3282 helix: 1.25 (0.20), residues: 693 sheet: 0.25 (0.18), residues: 768 loop : -1.10 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 152 HIS 0.003 0.001 HIS C1101 PHE 0.015 0.002 PHE B 541 TYR 0.030 0.002 TYR C 904 ARG 0.019 0.001 ARG A 847 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7458 (p-80) REVERT: A 169 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: B 21 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7863 (mtm180) REVERT: B 271 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: B 697 MET cc_start: 0.8524 (ptm) cc_final: 0.8237 (ptm) REVERT: B 1038 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8119 (mmtp) REVERT: C 176 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7860 (mm) REVERT: C 271 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: C 900 MET cc_start: 0.8710 (mtp) cc_final: 0.8452 (mtt) outliers start: 43 outliers final: 30 residues processed: 194 average time/residue: 1.2456 time to fit residues: 289.3474 Evaluate side-chains 198 residues out of total 2877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 0.0060 chunk 80 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 675 GLN B1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.086978 restraints weight = 37878.066| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.22 r_work: 0.2922 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 27921 Z= 0.140 Angle : 0.493 9.855 37935 Z= 0.253 Chirality : 0.042 0.175 4542 Planarity : 0.003 0.080 4776 Dihedral : 7.420 107.698 5637 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.46 % Allowed : 14.15 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3282 helix: 1.58 (0.20), residues: 693 sheet: 0.27 (0.18), residues: 774 loop : -1.06 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 152 HIS 0.002 0.000 HIS C 146 PHE 0.008 0.001 PHE C 133 TYR 0.024 0.001 TYR B 904 ARG 0.020 0.001 ARG A 847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7826.02 seconds wall clock time: 142 minutes 17.01 seconds (8537.01 seconds total)