Starting phenix.real_space_refine on Sun Apr 14 08:05:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czp_30512/04_2024/7czp_30512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czp_30512/04_2024/7czp_30512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czp_30512/04_2024/7czp_30512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czp_30512/04_2024/7czp_30512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czp_30512/04_2024/7czp_30512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czp_30512/04_2024/7czp_30512.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 127 5.16 5 C 19641 2.51 5 N 5038 2.21 5 O 6140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 219": "OE1" <-> "OE2" Residue "N GLU 164": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30946 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1669 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 15, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 14, 'TRANS': 198} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1669 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 15, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 14, 'TRANS': 198} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "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: "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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.64, per 1000 atoms: 0.51 Number of scatterers: 30946 At special positions: 0 Unit cell: (135.875, 165.224, 243.488, 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 127 16.00 O 6140 8.00 N 5038 7.00 C 19641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.14 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.14 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=2.08 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " 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 B1410 " - " NAG B1411 " " 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 I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN L 96 " " NAG d 1 " - " ASN N 96 " Time building additional restraints: 10.67 Conformation dependent library (CDL) restraints added in 5.5 seconds 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7216 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 65 sheets defined 19.7% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.855A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.631A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.641A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.855A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 194 through 197 removed outlier: 3.895A pdb=" N GLY H 197 " --> pdb=" O SER H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 194 through 197' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 192 Processing helix chain 'J' and resid 60 through 64 Processing helix chain 'J' and resid 194 through 197 removed outlier: 3.894A pdb=" N GLY J 197 " --> pdb=" O SER J 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 194 through 197' Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 185 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.446A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.843A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.712A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.780A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.573A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.843A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.643A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 37 through 39 Processing sheet with id=AF1, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.081A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 138 through 139 removed outlier: 6.081A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.323A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.454A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF6, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.462A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 118 through 122 removed outlier: 6.160A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 118 through 122 removed outlier: 6.160A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 149 through 154 Processing sheet with id=AG1, first strand: chain 'J' and resid 17 through 21 removed outlier: 3.644A pdb=" N LEU J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 37 through 39 Processing sheet with id=AG3, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.081A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 138 through 139 removed outlier: 6.081A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.323A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.454A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'N' and resid 17 through 23 Processing sheet with id=AG8, first strand: chain 'N' and resid 47 through 51 removed outlier: 6.462A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.160A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.160A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 149 through 154 1175 hydrogen bonds defined for protein. 3180 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: 16.71 Time building geometry restraints manager: 11.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9611 1.34 - 1.46: 8173 1.46 - 1.59: 13689 1.59 - 1.72: 0 1.72 - 1.84: 158 Bond restraints: 31631 Sorted by residual: bond pdb=" N PRO J 103 " pdb=" CD PRO J 103 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" N PRO H 103 " pdb=" CD PRO H 103 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.96e+01 bond pdb=" C ARG L 56 " pdb=" N PRO L 57 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.32e-02 5.74e+03 1.90e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" C ARG N 56 " pdb=" N PRO N 57 " ideal model delta sigma weight residual 1.332 1.388 -0.057 1.32e-02 5.74e+03 1.84e+01 ... (remaining 31626 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.75: 703 105.75 - 114.00: 18591 114.00 - 122.24: 18134 122.24 - 130.49: 5516 130.49 - 138.73: 102 Bond angle restraints: 43046 Sorted by residual: angle pdb=" N CYS C 538 " pdb=" CA CYS C 538 " pdb=" C CYS C 538 " ideal model delta sigma weight residual 110.10 100.86 9.24 1.49e+00 4.50e-01 3.85e+01 angle pdb=" N SER L 191 " pdb=" CA SER L 191 " pdb=" C SER L 191 " ideal model delta sigma weight residual 111.14 117.81 -6.67 1.08e+00 8.57e-01 3.82e+01 angle pdb=" N SER N 191 " pdb=" CA SER N 191 " pdb=" C SER N 191 " ideal model delta sigma weight residual 111.14 117.79 -6.65 1.08e+00 8.57e-01 3.79e+01 angle pdb=" N SER N 118 " pdb=" CA SER N 118 " pdb=" C SER N 118 " ideal model delta sigma weight residual 108.96 99.40 9.56 1.59e+00 3.96e-01 3.61e+01 angle pdb=" N SER L 118 " pdb=" CA SER L 118 " pdb=" C SER L 118 " ideal model delta sigma weight residual 108.96 99.40 9.56 1.59e+00 3.96e-01 3.61e+01 ... (remaining 43041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17002 17.92 - 35.84: 1955 35.84 - 53.76: 606 53.76 - 71.69: 202 71.69 - 89.61: 57 Dihedral angle restraints: 19822 sinusoidal: 8603 harmonic: 11219 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.13 80.87 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.58 73.42 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 5105 0.336 - 0.672: 4 0.672 - 1.009: 3 1.009 - 1.345: 2 1.345 - 1.681: 3 Chirality restraints: 5117 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.06e+03 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 -0.72 -1.68 2.00e-02 2.50e+03 7.05e+03 chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.15e+03 ... (remaining 5114 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.192 2.00e-02 2.50e+03 1.95e-01 4.73e+02 pdb=" CG ASN A 331 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.294 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.108 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" CG ASN C 331 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU J 155 " -0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO J 156 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO J 156 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 156 " -0.050 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 433 2.57 - 3.15: 25031 3.15 - 3.73: 45061 3.73 - 4.32: 65758 4.32 - 4.90: 109201 Nonbonded interactions: 245484 Sorted by model distance: nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.981 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 2.520 nonbonded pdb=" O PRO H 14 " pdb=" OG SER H 15 " model vdw 2.020 2.440 nonbonded pdb=" O PRO J 14 " pdb=" OG SER J 15 " model vdw 2.020 2.440 nonbonded pdb=" O SER J 15 " pdb=" OE2 GLU J 16 " model vdw 2.127 3.040 ... (remaining 245479 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 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 11 \ 46 or resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1146 or resid 1401 through \ 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' 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' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.170 Check model and map are aligned: 0.470 Set scattering table: 0.310 Process input model: 81.750 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.380 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 0.118 31631 Z= 0.738 Angle : 1.030 13.734 43046 Z= 0.583 Chirality : 0.079 1.681 5117 Planarity : 0.007 0.094 5440 Dihedral : 17.808 89.607 12468 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 1.87 % Allowed : 11.41 % Favored : 86.72 % Rotamer: Outliers : 13.35 % Allowed : 20.24 % Favored : 66.41 % 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: -3.91 (0.11), residues: 3794 helix: -2.20 (0.16), residues: 703 sheet: -1.78 (0.14), residues: 1137 loop : -3.32 (0.11), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 104 HIS 0.009 0.001 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.027 0.003 TYR B1067 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 449 poor density : 376 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5559 (p0) REVERT: A 394 ASN cc_start: 0.4465 (m-40) cc_final: 0.4219 (m-40) REVERT: A 544 ASN cc_start: 0.8130 (p0) cc_final: 0.7772 (t0) REVERT: A 787 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: A 1018 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9040 (tp) REVERT: A 1039 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8465 (mtp180) REVERT: B 66 HIS cc_start: 0.4867 (OUTLIER) cc_final: 0.4582 (m-70) REVERT: B 99 ASN cc_start: 0.6306 (OUTLIER) cc_final: 0.5720 (p0) REVERT: B 158 ARG cc_start: 0.4610 (mmt90) cc_final: 0.4278 (mmm160) REVERT: B 418 ILE cc_start: 0.5873 (OUTLIER) cc_final: 0.5518 (mm) REVERT: B 640 SER cc_start: 0.3866 (OUTLIER) cc_final: 0.3516 (t) REVERT: B 747 THR cc_start: 0.8309 (p) cc_final: 0.8028 (m) REVERT: B 811 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5073 (tmtt) REVERT: B 1030 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9064 (m) REVERT: C 417 LYS cc_start: 0.2999 (OUTLIER) cc_final: 0.1837 (tmtt) REVERT: C 514 SER cc_start: 0.3711 (OUTLIER) cc_final: 0.3269 (m) REVERT: C 553 THR cc_start: 0.5446 (OUTLIER) cc_final: 0.4990 (m) REVERT: C 985 ASP cc_start: 0.6979 (p0) cc_final: 0.6773 (p0) REVERT: H 57 THR cc_start: 0.0487 (OUTLIER) cc_final: 0.0264 (t) REVERT: L 68 LYS cc_start: 0.3271 (OUTLIER) cc_final: 0.2488 (tmtm) REVERT: L 199 VAL cc_start: -0.1437 (OUTLIER) cc_final: -0.1708 (p) REVERT: J 29 ILE cc_start: -0.0191 (OUTLIER) cc_final: -0.0613 (tt) REVERT: J 85 VAL cc_start: 0.2725 (OUTLIER) cc_final: 0.2475 (t) REVERT: N 90 CYS cc_start: 0.0934 (OUTLIER) cc_final: -0.0116 (t) outliers start: 449 outliers final: 91 residues processed: 775 average time/residue: 1.0293 time to fit residues: 995.3953 Evaluate side-chains 299 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 189 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 207 HIS Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 152 TRP Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain N residue 96 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 134 GLN A 137 ASN A 164 ASN A 188 ASN A 207 HIS A 314 GLN A 360 ASN A 394 ASN A 422 ASN A 440 ASN A 498 GLN A 613 GLN A 644 GLN A 690 GLN A 703 ASN A 762 GLN A 787 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 935 GLN A 955 ASN A 969 ASN A 992 GLN A1101 HIS A1125 ASN A1142 GLN B 87 ASN B 115 GLN B 134 GLN B 164 ASN B 188 ASN B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 540 ASN B 563 GLN B 703 ASN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 935 GLN B 992 GLN B1002 GLN B1005 GLN B1054 GLN C 30 ASN C 134 GLN C 207 HIS C 422 ASN C 440 ASN C 498 GLN C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1005 GLN C1071 GLN C1101 HIS L 39 GLN L 132 ASN L 174 ASN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 39 GLN N 132 ASN N 174 ASN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31631 Z= 0.242 Angle : 0.787 13.435 43046 Z= 0.393 Chirality : 0.051 0.595 5117 Planarity : 0.006 0.109 5440 Dihedral : 9.993 72.563 5835 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.20 % Favored : 91.35 % Rotamer: Outliers : 7.49 % Allowed : 23.31 % Favored : 69.20 % 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: -2.55 (0.12), residues: 3794 helix: -0.13 (0.19), residues: 703 sheet: -1.16 (0.15), residues: 1118 loop : -2.68 (0.12), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 102 HIS 0.006 0.001 HIS C 519 PHE 0.031 0.002 PHE J 153 TYR 0.032 0.002 TYR H 50 ARG 0.013 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 214 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.3144 (OUTLIER) cc_final: 0.2324 (m-70) REVERT: A 202 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6751 (ttmm) REVERT: A 389 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5417 (p0) REVERT: A 544 ASN cc_start: 0.8109 (p0) cc_final: 0.7878 (t0) REVERT: A 975 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 52 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7579 (tp40) REVERT: B 99 ASN cc_start: 0.6419 (OUTLIER) cc_final: 0.5757 (p0) REVERT: B 158 ARG cc_start: 0.4858 (OUTLIER) cc_final: 0.4493 (mmm160) REVERT: B 747 THR cc_start: 0.8168 (p) cc_final: 0.7923 (m) REVERT: B 867 ASP cc_start: 0.7122 (p0) cc_final: 0.6914 (p0) REVERT: C 153 MET cc_start: 0.4331 (OUTLIER) cc_final: 0.3904 (tmm) REVERT: C 417 LYS cc_start: 0.3145 (OUTLIER) cc_final: 0.1894 (tppt) REVERT: C 532 ASN cc_start: 0.5598 (OUTLIER) cc_final: 0.5185 (m-40) REVERT: C 964 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8442 (mtmm) REVERT: C 985 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6756 (p0) REVERT: C 988 GLU cc_start: 0.6814 (mp0) cc_final: 0.6586 (mp0) REVERT: C 1017 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: H 17 THR cc_start: 0.1784 (OUTLIER) cc_final: 0.1289 (p) REVERT: H 64 LYS cc_start: 0.2601 (tptt) cc_final: 0.1576 (mttt) REVERT: L 49 MET cc_start: 0.1789 (mmm) cc_final: 0.0780 (tpt) REVERT: L 148 VAL cc_start: 0.0736 (m) cc_final: 0.0433 (t) REVERT: L 199 VAL cc_start: -0.1402 (OUTLIER) cc_final: -0.1813 (p) REVERT: J 101 ASP cc_start: 0.2710 (OUTLIER) cc_final: 0.1236 (p0) REVERT: N 180 SER cc_start: 0.0749 (OUTLIER) cc_final: 0.0457 (p) outliers start: 252 outliers final: 99 residues processed: 440 average time/residue: 0.9678 time to fit residues: 546.1071 Evaluate side-chains 285 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 169 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 0.0040 chunk 349 optimal weight: 20.0000 chunk 377 optimal weight: 30.0000 chunk 311 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 540 ASN A 655 HIS A 762 GLN A 824 ASN A1011 GLN B 99 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C1005 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 201 HIS ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 31631 Z= 0.361 Angle : 0.803 12.907 43046 Z= 0.398 Chirality : 0.053 0.658 5117 Planarity : 0.005 0.059 5440 Dihedral : 8.963 59.847 5735 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.59 % Favored : 90.99 % Rotamer: Outliers : 6.69 % Allowed : 24.29 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 3794 helix: 0.40 (0.20), residues: 695 sheet: -0.75 (0.15), residues: 1069 loop : -2.39 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP J 102 HIS 0.009 0.002 HIS B1048 PHE 0.029 0.002 PHE H 78 TYR 0.023 0.002 TYR A 265 ARG 0.008 0.001 ARG N 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 190 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER H 120 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 169 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5612 (tp30) REVERT: A 569 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7524 (mt) REVERT: A 975 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 52 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: B 99 ASN cc_start: 0.6536 (OUTLIER) cc_final: 0.6044 (p0) REVERT: B 158 ARG cc_start: 0.5070 (mmt90) cc_final: 0.4687 (mmm160) REVERT: B 214 ARG cc_start: 0.2325 (OUTLIER) cc_final: 0.0894 (mtp180) REVERT: B 414 GLN cc_start: 0.4677 (OUTLIER) cc_final: 0.4017 (pt0) REVERT: B 699 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8591 (mp) REVERT: C 153 MET cc_start: 0.4763 (OUTLIER) cc_final: 0.4458 (tmm) REVERT: C 532 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5356 (m-40) REVERT: C 567 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7718 (mtt-85) REVERT: C 964 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8480 (mtmm) REVERT: C 985 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6814 (t0) REVERT: H 17 THR cc_start: 0.2043 (OUTLIER) cc_final: 0.1568 (p) REVERT: H 212 THR cc_start: 0.1795 (OUTLIER) cc_final: 0.1428 (m) REVERT: L 49 MET cc_start: 0.1599 (mmm) cc_final: 0.0383 (tmm) REVERT: L 199 VAL cc_start: -0.1252 (OUTLIER) cc_final: -0.1532 (p) REVERT: J 104 LEU cc_start: 0.1811 (OUTLIER) cc_final: 0.1432 (tp) REVERT: N 1 GLN cc_start: 0.3079 (OUTLIER) cc_final: 0.2695 (pp30) REVERT: N 81 GLN cc_start: 0.1022 (OUTLIER) cc_final: 0.0369 (mp-120) outliers start: 225 outliers final: 120 residues processed: 393 average time/residue: 0.9520 time to fit residues: 476.8909 Evaluate side-chains 298 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 159 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 239 GLN C1005 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 201 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31631 Z= 0.260 Angle : 0.709 11.115 43046 Z= 0.348 Chirality : 0.050 0.675 5117 Planarity : 0.005 0.050 5440 Dihedral : 8.484 59.809 5721 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.22 % Favored : 92.38 % Rotamer: Outliers : 5.98 % Allowed : 24.88 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3794 helix: 0.76 (0.21), residues: 693 sheet: -0.49 (0.15), residues: 1094 loop : -2.22 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 102 HIS 0.005 0.001 HIS B1048 PHE 0.023 0.002 PHE B 168 TYR 0.020 0.001 TYR B 28 ARG 0.008 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 174 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4192 (p90) REVERT: A 518 LEU cc_start: 0.4206 (OUTLIER) cc_final: 0.3983 (pt) REVERT: A 569 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7837 (mt) REVERT: A 1002 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: B 52 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7594 (tp40) REVERT: B 99 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6110 (p0) REVERT: B 158 ARG cc_start: 0.5167 (mmt90) cc_final: 0.4734 (mmm160) REVERT: B 414 GLN cc_start: 0.4911 (OUTLIER) cc_final: 0.4162 (mp10) REVERT: B 565 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7439 (p90) REVERT: B 787 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8116 (mt0) REVERT: B 811 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.6109 (mmtm) REVERT: B 981 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7836 (tp) REVERT: B 1045 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8608 (ttpt) REVERT: C 269 TYR cc_start: 0.6474 (m-80) cc_final: 0.5933 (m-80) REVERT: C 567 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: C 1045 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8443 (tttm) REVERT: H 109 ILE cc_start: 0.4988 (OUTLIER) cc_final: 0.4023 (mt) REVERT: H 115 MET cc_start: 0.3488 (OUTLIER) cc_final: 0.2197 (mpt) REVERT: H 212 THR cc_start: 0.1716 (OUTLIER) cc_final: 0.1361 (m) REVERT: L 6 GLN cc_start: 0.3464 (OUTLIER) cc_final: 0.2739 (tt0) REVERT: L 49 MET cc_start: 0.1740 (mmm) cc_final: 0.0713 (tmm) REVERT: L 148 VAL cc_start: 0.1165 (m) cc_final: 0.0879 (t) REVERT: L 199 VAL cc_start: -0.1292 (OUTLIER) cc_final: -0.1688 (p) REVERT: N 1 GLN cc_start: 0.3282 (OUTLIER) cc_final: 0.2849 (pp30) REVERT: N 38 TYR cc_start: 0.3027 (m-80) cc_final: 0.2425 (m-80) REVERT: N 165 THR cc_start: 0.0921 (OUTLIER) cc_final: 0.0647 (p) outliers start: 201 outliers final: 109 residues processed: 352 average time/residue: 1.0012 time to fit residues: 448.1634 Evaluate side-chains 284 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 154 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 30.0000 chunk 210 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.5980 chunk 333 optimal weight: 30.0000 chunk 93 optimal weight: 0.3980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 955 ASN B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 658 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 31631 Z= 0.434 Angle : 0.822 19.905 43046 Z= 0.401 Chirality : 0.055 0.738 5117 Planarity : 0.005 0.069 5440 Dihedral : 8.730 59.943 5717 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.88 % Favored : 90.75 % Rotamer: Outliers : 6.93 % Allowed : 24.02 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3794 helix: 0.42 (0.20), residues: 712 sheet: -0.61 (0.15), residues: 1099 loop : -2.21 (0.12), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 102 HIS 0.008 0.002 HIS B1048 PHE 0.025 0.002 PHE A 238 TYR 0.024 0.002 TYR A 265 ARG 0.005 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 167 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER J 120 " (corrupted residue). Skipping it. REVERT: A 140 PHE cc_start: 0.5378 (OUTLIER) cc_final: 0.4625 (p90) REVERT: A 518 LEU cc_start: 0.4353 (OUTLIER) cc_final: 0.4109 (pt) REVERT: A 569 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7952 (mt) REVERT: A 1002 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: B 52 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7603 (tp40) REVERT: B 99 ASN cc_start: 0.6755 (OUTLIER) cc_final: 0.6205 (p0) REVERT: B 117 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7704 (tp) REVERT: B 153 MET cc_start: 0.2129 (tmt) cc_final: 0.1904 (ttt) REVERT: B 158 ARG cc_start: 0.5240 (mmt90) cc_final: 0.4782 (mmm160) REVERT: B 214 ARG cc_start: 0.2933 (OUTLIER) cc_final: 0.2582 (pmt-80) REVERT: B 699 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 811 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6175 (mttt) REVERT: B 994 ASP cc_start: 0.7927 (t0) cc_final: 0.7658 (t0) REVERT: B 1045 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8750 (ttpt) REVERT: C 472 ILE cc_start: 0.2007 (OUTLIER) cc_final: 0.1017 (mp) REVERT: C 567 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7923 (mtt-85) REVERT: C 794 ILE cc_start: 0.8367 (tp) cc_final: 0.8106 (pt) REVERT: C 1045 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8567 (tttm) REVERT: H 109 ILE cc_start: 0.5129 (OUTLIER) cc_final: 0.4175 (mt) REVERT: H 212 THR cc_start: 0.1535 (OUTLIER) cc_final: 0.1125 (m) REVERT: L 6 GLN cc_start: 0.3651 (OUTLIER) cc_final: 0.3330 (tt0) REVERT: L 49 MET cc_start: 0.1839 (mmm) cc_final: 0.0818 (tmm) REVERT: L 50 ILE cc_start: 0.1302 (OUTLIER) cc_final: 0.0991 (pt) REVERT: L 68 LYS cc_start: 0.2619 (OUTLIER) cc_final: 0.1229 (tmtm) REVERT: L 199 VAL cc_start: -0.1272 (OUTLIER) cc_final: -0.1498 (p) REVERT: N 1 GLN cc_start: 0.3303 (OUTLIER) cc_final: 0.2832 (pp30) REVERT: N 38 TYR cc_start: 0.2994 (m-80) cc_final: 0.2323 (m-80) REVERT: N 81 GLN cc_start: 0.1672 (OUTLIER) cc_final: 0.0949 (mp-120) outliers start: 233 outliers final: 139 residues processed: 376 average time/residue: 0.9732 time to fit residues: 464.3873 Evaluate side-chains 310 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 149 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 542 ASN A 762 GLN A 955 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 31631 Z= 0.189 Angle : 0.689 15.996 43046 Z= 0.336 Chirality : 0.051 1.124 5117 Planarity : 0.004 0.057 5440 Dihedral : 8.287 59.802 5716 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.91 % Favored : 92.78 % Rotamer: Outliers : 5.02 % Allowed : 26.34 % Favored : 68.64 % Cbeta Deviations : 0.03 % 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: -1.40 (0.13), residues: 3794 helix: 0.87 (0.20), residues: 711 sheet: -0.26 (0.16), residues: 1067 loop : -2.05 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 102 HIS 0.003 0.001 HIS C 66 PHE 0.022 0.001 PHE A 486 TYR 0.019 0.001 TYR H 33 ARG 0.008 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 171 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER J 120 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 140 PHE cc_start: 0.5164 (p90) cc_final: 0.4475 (p90) REVERT: A 569 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (mt) REVERT: B 52 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7602 (tp40) REVERT: B 158 ARG cc_start: 0.5161 (mmt90) cc_final: 0.4793 (mmm160) REVERT: B 414 GLN cc_start: 0.5450 (OUTLIER) cc_final: 0.4662 (mp10) REVERT: B 697 MET cc_start: 0.8279 (ptm) cc_final: 0.7951 (ptm) REVERT: B 811 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6285 (mmtm) REVERT: B 994 ASP cc_start: 0.7628 (t0) cc_final: 0.7311 (t0) REVERT: B 1045 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8679 (mmtt) REVERT: C 195 LYS cc_start: 0.7113 (ptmt) cc_final: 0.6873 (ttpt) REVERT: C 269 TYR cc_start: 0.6595 (m-80) cc_final: 0.5940 (m-80) REVERT: C 472 ILE cc_start: 0.2172 (OUTLIER) cc_final: 0.1329 (mp) REVERT: C 518 LEU cc_start: 0.4302 (OUTLIER) cc_final: 0.3949 (mp) REVERT: C 567 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7656 (mtt-85) REVERT: H 109 ILE cc_start: 0.5025 (OUTLIER) cc_final: 0.3797 (mm) REVERT: L 6 GLN cc_start: 0.3541 (OUTLIER) cc_final: 0.2777 (tt0) REVERT: L 49 MET cc_start: 0.2124 (mmm) cc_final: 0.0997 (tmm) REVERT: L 50 ILE cc_start: 0.1391 (OUTLIER) cc_final: 0.1130 (pt) REVERT: L 68 LYS cc_start: 0.2328 (OUTLIER) cc_final: 0.0904 (tmtm) REVERT: L 180 SER cc_start: 0.0932 (OUTLIER) cc_final: 0.0713 (m) REVERT: L 199 VAL cc_start: -0.1352 (OUTLIER) cc_final: -0.1562 (p) REVERT: N 38 TYR cc_start: 0.3043 (m-80) cc_final: 0.2499 (m-80) REVERT: N 81 GLN cc_start: 0.1643 (OUTLIER) cc_final: 0.1015 (mp-120) outliers start: 169 outliers final: 100 residues processed: 323 average time/residue: 1.0512 time to fit residues: 424.5658 Evaluate side-chains 273 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 158 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 271 optimal weight: 0.7980 chunk 210 optimal weight: 0.6980 chunk 312 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 370 optimal weight: 50.0000 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 31631 Z= 0.199 Angle : 0.680 14.124 43046 Z= 0.327 Chirality : 0.048 0.579 5117 Planarity : 0.004 0.049 5440 Dihedral : 7.970 59.217 5702 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.75 % Favored : 91.93 % Rotamer: Outliers : 4.85 % Allowed : 26.04 % Favored : 69.11 % 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: -1.25 (0.13), residues: 3794 helix: 1.09 (0.21), residues: 714 sheet: -0.26 (0.16), residues: 1094 loop : -1.95 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 102 HIS 0.003 0.001 HIS B1048 PHE 0.024 0.001 PHE A 486 TYR 0.018 0.001 TYR H 33 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 178 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER J 120 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 140 PHE cc_start: 0.5587 (p90) cc_final: 0.4875 (p90) REVERT: A 569 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8007 (mt) REVERT: B 52 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7426 (tp-100) REVERT: B 158 ARG cc_start: 0.5085 (mmt90) cc_final: 0.4764 (mmm160) REVERT: B 314 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 414 GLN cc_start: 0.5457 (OUTLIER) cc_final: 0.4669 (mp10) REVERT: B 787 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: B 811 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6229 (mmtm) REVERT: B 994 ASP cc_start: 0.7701 (t0) cc_final: 0.7398 (t0) REVERT: B 1045 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8630 (ttpt) REVERT: C 195 LYS cc_start: 0.7153 (ptmt) cc_final: 0.6952 (ttpt) REVERT: C 216 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.4852 (tt) REVERT: C 269 TYR cc_start: 0.6622 (m-80) cc_final: 0.6155 (m-80) REVERT: C 472 ILE cc_start: 0.2025 (OUTLIER) cc_final: 0.1144 (mp) REVERT: C 518 LEU cc_start: 0.4226 (OUTLIER) cc_final: 0.3906 (mp) REVERT: C 567 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7699 (mtt-85) REVERT: H 109 ILE cc_start: 0.5068 (OUTLIER) cc_final: 0.3838 (mm) REVERT: H 212 THR cc_start: 0.1738 (OUTLIER) cc_final: 0.1314 (m) REVERT: L 6 GLN cc_start: 0.3500 (OUTLIER) cc_final: 0.2711 (tt0) REVERT: L 49 MET cc_start: 0.2104 (mmm) cc_final: 0.1023 (tmm) REVERT: L 50 ILE cc_start: 0.1361 (OUTLIER) cc_final: 0.1099 (pt) REVERT: L 68 LYS cc_start: 0.2036 (OUTLIER) cc_final: 0.0862 (tmtm) REVERT: L 180 SER cc_start: 0.0986 (OUTLIER) cc_final: 0.0775 (m) REVERT: L 199 VAL cc_start: -0.1331 (OUTLIER) cc_final: -0.1535 (p) REVERT: N 38 TYR cc_start: 0.3152 (m-80) cc_final: 0.2757 (m-80) REVERT: N 51 TYR cc_start: 0.2944 (OUTLIER) cc_final: 0.2101 (p90) REVERT: N 81 GLN cc_start: 0.1923 (OUTLIER) cc_final: 0.1197 (mp-120) outliers start: 163 outliers final: 107 residues processed: 321 average time/residue: 1.0366 time to fit residues: 420.4174 Evaluate side-chains 292 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 165 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 762 GLN A1142 GLN B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 31631 Z= 0.186 Angle : 0.663 15.477 43046 Z= 0.321 Chirality : 0.048 0.621 5117 Planarity : 0.004 0.048 5440 Dihedral : 7.566 59.857 5697 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.85 % Favored : 92.86 % Rotamer: Outliers : 4.40 % Allowed : 26.28 % Favored : 69.32 % 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: -1.15 (0.13), residues: 3794 helix: 1.20 (0.21), residues: 710 sheet: -0.21 (0.16), residues: 1091 loop : -1.89 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 102 HIS 0.003 0.001 HIS B1048 PHE 0.022 0.001 PHE A 486 TYR 0.016 0.001 TYR H 33 ARG 0.010 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 169 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER H 120 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER J 120 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 140 PHE cc_start: 0.5607 (p90) cc_final: 0.4902 (p90) REVERT: A 389 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6429 (m-30) REVERT: A 569 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8000 (mt) REVERT: B 52 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7523 (tp-100) REVERT: B 158 ARG cc_start: 0.5105 (mmt90) cc_final: 0.4785 (mmm160) REVERT: B 314 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: B 414 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.4666 (mp10) REVERT: B 697 MET cc_start: 0.8239 (ptm) cc_final: 0.7946 (ptm) REVERT: B 811 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6278 (mmtm) REVERT: B 994 ASP cc_start: 0.7659 (t0) cc_final: 0.7349 (t0) REVERT: B 1045 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8628 (ttpt) REVERT: C 269 TYR cc_start: 0.6629 (m-80) cc_final: 0.6174 (m-80) REVERT: C 518 LEU cc_start: 0.4308 (OUTLIER) cc_final: 0.3909 (mt) REVERT: C 567 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7692 (mtt-85) REVERT: H 109 ILE cc_start: 0.4999 (OUTLIER) cc_final: 0.3801 (mm) REVERT: H 212 THR cc_start: 0.1724 (OUTLIER) cc_final: 0.1296 (m) REVERT: L 49 MET cc_start: 0.2096 (mmm) cc_final: 0.0987 (tmm) REVERT: L 50 ILE cc_start: 0.1457 (OUTLIER) cc_final: 0.1095 (pt) REVERT: L 68 LYS cc_start: 0.2018 (OUTLIER) cc_final: 0.0819 (tmtm) REVERT: L 180 SER cc_start: 0.1012 (OUTLIER) cc_final: 0.0802 (m) REVERT: N 1 GLN cc_start: 0.2746 (OUTLIER) cc_final: 0.2408 (pp30) REVERT: N 38 TYR cc_start: 0.2964 (m-80) cc_final: 0.2615 (m-80) REVERT: N 81 GLN cc_start: 0.1935 (OUTLIER) cc_final: 0.1229 (mp-120) outliers start: 148 outliers final: 106 residues processed: 300 average time/residue: 1.0495 time to fit residues: 396.0445 Evaluate side-chains 284 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 162 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 9.9990 chunk 354 optimal weight: 0.4980 chunk 323 optimal weight: 7.9990 chunk 344 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 343 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 762 GLN A1142 GLN B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 31631 Z= 0.251 Angle : 0.683 15.141 43046 Z= 0.332 Chirality : 0.049 0.634 5117 Planarity : 0.004 0.048 5440 Dihedral : 7.505 59.179 5694 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.56 % Favored : 92.17 % Rotamer: Outliers : 4.55 % Allowed : 26.04 % Favored : 69.41 % 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: -1.16 (0.13), residues: 3794 helix: 1.22 (0.21), residues: 698 sheet: -0.21 (0.16), residues: 1077 loop : -1.88 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 102 HIS 0.005 0.001 HIS B1048 PHE 0.021 0.002 PHE A 238 TYR 0.017 0.001 TYR C1067 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 169 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER H 120 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER J 120 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 161 SER cc_start: 0.4459 (OUTLIER) cc_final: 0.3998 (p) REVERT: A 569 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 158 ARG cc_start: 0.5086 (mmt90) cc_final: 0.4770 (mmm160) REVERT: B 314 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: B 390 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7539 (mt) REVERT: B 787 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: B 811 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6052 (mmtm) REVERT: B 1045 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8658 (ttpt) REVERT: C 269 TYR cc_start: 0.6684 (m-80) cc_final: 0.6182 (m-80) REVERT: C 472 ILE cc_start: 0.1962 (OUTLIER) cc_final: 0.1134 (mp) REVERT: C 518 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.3893 (mt) REVERT: C 533 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7291 (pt) REVERT: C 567 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7856 (mtt-85) REVERT: H 109 ILE cc_start: 0.5157 (OUTLIER) cc_final: 0.3951 (mm) REVERT: H 212 THR cc_start: 0.1735 (OUTLIER) cc_final: 0.1279 (m) REVERT: L 6 GLN cc_start: 0.3351 (OUTLIER) cc_final: 0.3121 (tt0) REVERT: L 49 MET cc_start: 0.1974 (mmm) cc_final: 0.0771 (tmm) REVERT: L 50 ILE cc_start: 0.1466 (OUTLIER) cc_final: 0.1081 (pt) REVERT: N 1 GLN cc_start: 0.2642 (OUTLIER) cc_final: 0.2385 (pp30) REVERT: N 38 TYR cc_start: 0.3004 (m-80) cc_final: 0.2796 (m-80) REVERT: N 51 TYR cc_start: 0.2767 (OUTLIER) cc_final: 0.1948 (p90) outliers start: 153 outliers final: 109 residues processed: 306 average time/residue: 1.1188 time to fit residues: 435.6510 Evaluate side-chains 287 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 161 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 5.9990 chunk 364 optimal weight: 0.5980 chunk 222 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 382 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 304 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 762 GLN A1142 GLN B 30 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 31631 Z= 0.190 Angle : 0.662 22.809 43046 Z= 0.319 Chirality : 0.048 0.580 5117 Planarity : 0.004 0.047 5440 Dihedral : 7.251 59.370 5690 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.62 % Favored : 93.12 % Rotamer: Outliers : 3.89 % Allowed : 26.75 % Favored : 69.35 % 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: -1.04 (0.13), residues: 3794 helix: 1.35 (0.21), residues: 698 sheet: -0.12 (0.16), residues: 1085 loop : -1.83 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 34 HIS 0.003 0.001 HIS B1048 PHE 0.020 0.001 PHE A 486 TYR 0.016 0.001 TYR C1067 ARG 0.010 0.000 ARG H 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 167 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER H 120 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER J 120 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 161 SER cc_start: 0.4903 (OUTLIER) cc_final: 0.4393 (p) REVERT: A 569 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 158 ARG cc_start: 0.5105 (mmt90) cc_final: 0.4778 (mmm160) REVERT: B 314 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: B 390 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7541 (mt) REVERT: B 414 GLN cc_start: 0.5544 (OUTLIER) cc_final: 0.4485 (pm20) REVERT: B 787 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: B 1045 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8642 (mmtt) REVERT: C 269 TYR cc_start: 0.6649 (m-80) cc_final: 0.6187 (m-80) REVERT: C 518 LEU cc_start: 0.4296 (OUTLIER) cc_final: 0.3913 (mt) REVERT: C 567 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7774 (mtt-85) REVERT: H 109 ILE cc_start: 0.4954 (OUTLIER) cc_final: 0.3799 (mm) REVERT: H 212 THR cc_start: 0.1346 (OUTLIER) cc_final: 0.0915 (m) REVERT: L 49 MET cc_start: 0.2003 (mmm) cc_final: 0.0903 (tmm) REVERT: L 50 ILE cc_start: 0.1779 (OUTLIER) cc_final: 0.1432 (pt) REVERT: J 115 MET cc_start: -0.0282 (tpt) cc_final: -0.0941 (mmt) REVERT: N 51 TYR cc_start: 0.2485 (OUTLIER) cc_final: 0.1877 (p90) outliers start: 131 outliers final: 98 residues processed: 285 average time/residue: 1.0424 time to fit residues: 379.4119 Evaluate side-chains 271 residues out of total 3364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 160 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 762 GLN A 955 ASN A1142 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 613 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.203885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161336 restraints weight = 45238.243| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.51 r_work: 0.3565 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 31631 Z= 0.339 Angle : 0.732 22.844 43046 Z= 0.355 Chirality : 0.051 0.672 5117 Planarity : 0.005 0.052 5440 Dihedral : 7.651 59.522 5689 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.25 % Favored : 91.51 % Rotamer: Outliers : 3.95 % Allowed : 26.66 % Favored : 69.38 % 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: -1.21 (0.13), residues: 3794 helix: 1.05 (0.21), residues: 697 sheet: -0.19 (0.16), residues: 1071 loop : -1.89 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 102 HIS 0.006 0.001 HIS B1048 PHE 0.024 0.002 PHE A 238 TYR 0.025 0.002 TYR A 369 ARG 0.006 0.001 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9110.77 seconds wall clock time: 177 minutes 10.24 seconds (10630.24 seconds total)