Starting phenix.real_space_refine on Fri Feb 23 03:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/02_2024/7x08_32920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/02_2024/7x08_32920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/02_2024/7x08_32920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/02_2024/7x08_32920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/02_2024/7x08_32920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/02_2024/7x08_32920_updated.pdb" } resolution = 2.7 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= 0.006 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 159 5.16 5 C 23067 2.51 5 N 5970 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 207": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "M GLU 187": "OE1" <-> "OE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "N GLU 164": "OE1" <-> "OE2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "N GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36396 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "I" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "M" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "J" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} 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: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 180 Unusual residues: {'EIC': 2, 'NAG': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 18.76, per 1000 atoms: 0.52 Number of scatterers: 36396 At special positions: 0 Unit cell: (185.877, 197.834, 217.4, 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 159 16.00 O 7200 8.00 N 5970 7.00 C 23067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.78 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=1.92 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.49 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.78 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.49 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=1.78 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.94 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.99 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 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 149 " - pdb=" SG CYS H 205 " 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=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 197 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 205 " 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1403 " - " ASN A 61 " " NAG A1404 " - " ASN A 122 " " NAG A1405 " - " ASN A 149 " " NAG A1406 " - " ASN A 165 " " NAG A1407 " - " ASN A 234 " " NAG A1408 " - " ASN A 282 " " NAG A1409 " - " ASN A 343 " " NAG A1410 " - " ASN A 603 " " NAG A1413 " - " ASN A 657 " " NAG A1414 " - " ASN A 709 " " NAG B1403 " - " ASN B 61 " " NAG B1404 " - " ASN B 122 " " NAG B1405 " - " ASN B 149 " " NAG B1406 " - " ASN B 165 " " NAG B1407 " - " ASN B 234 " " NAG B1408 " - " ASN B 282 " " NAG B1409 " - " ASN B 343 " " NAG B1410 " - " ASN B 603 " " NAG B1413 " - " ASN B 657 " " NAG B1414 " - " ASN B 709 " " NAG C1403 " - " ASN C 61 " " NAG C1404 " - " ASN C 122 " " NAG C1405 " - " ASN C 149 " " NAG C1406 " - " ASN C 165 " " NAG C1407 " - " ASN C 234 " " NAG C1408 " - " ASN C 282 " " NAG C1409 " - " ASN C 343 " " NAG C1410 " - " ASN C 603 " " NAG C1413 " - " ASN C 657 " " NAG C1414 " - " ASN C 709 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN C 331 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN A 616 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 17 " " NAG Y 1 " - " ASN B 616 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B1074 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C 17 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1074 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 13.82 Conformation dependent library (CDL) restraints added in 7.2 seconds 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 63 sheets defined 15.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.835A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.089A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.764A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.782A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.512A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.098A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.476A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.834A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.763A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 421' Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.785A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.510A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.098A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 981 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.834A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 389' Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.089A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.763A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 421' Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 removed outlier: 3.786A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 837 through 840 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.512A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.099A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 186 through 191 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'N' and resid 126 through 130 Processing helix chain 'N' and resid 186 through 191 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.208A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.490A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.688A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.207A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.897A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.756A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 242 through 247 removed outlier: 6.110A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.656A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.491A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.688A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.051A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AA, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.207A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AI, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.489A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.687A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AN, first strand: chain 'H' and resid 17 through 23 Processing sheet with id= AO, first strand: chain 'H' and resid 116 through 118 removed outlier: 5.542A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.990A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 159 through 163 Processing sheet with id= AR, first strand: chain 'L' and resid 17 through 21 Processing sheet with id= AS, first strand: chain 'L' and resid 90 through 92 removed outlier: 6.566A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 118 through 122 Processing sheet with id= AU, first strand: chain 'L' and resid 149 through 153 Processing sheet with id= AV, first strand: chain 'I' and resid 17 through 23 Processing sheet with id= AW, first strand: chain 'I' and resid 116 through 118 removed outlier: 5.541A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.990A pdb=" N TYR I 185 " --> pdb=" O ASP I 153 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 159 through 163 Processing sheet with id= AZ, first strand: chain 'M' and resid 17 through 21 Processing sheet with id= BA, first strand: chain 'M' and resid 90 through 92 removed outlier: 6.566A pdb=" N GLN M 39 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU M 48 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'M' and resid 118 through 122 Processing sheet with id= BC, first strand: chain 'M' and resid 149 through 153 Processing sheet with id= BD, first strand: chain 'J' and resid 17 through 23 Processing sheet with id= BE, first strand: chain 'J' and resid 116 through 118 removed outlier: 5.540A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.989A pdb=" N TYR J 185 " --> pdb=" O ASP J 153 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'J' and resid 159 through 163 Processing sheet with id= BH, first strand: chain 'N' and resid 17 through 21 Processing sheet with id= BI, first strand: chain 'N' and resid 90 through 92 removed outlier: 6.566A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= BK, first strand: chain 'N' and resid 149 through 153 1224 hydrogen bonds defined for protein. 3393 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: 14.96 Time building geometry restraints manager: 14.99 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: 11335 1.34 - 1.46: 9285 1.46 - 1.59: 16406 1.59 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 37230 Sorted by residual: bond pdb=" C GLY A 891 " pdb=" N PRO A 892 " ideal model delta sigma weight residual 1.329 1.390 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.26e-02 6.30e+03 2.21e+01 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.32e-02 5.74e+03 1.96e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.318 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.318 0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 37225 not shown) Histogram of bond angle deviations from ideal: 99.68 - 107.51: 1589 107.51 - 115.35: 22433 115.35 - 123.18: 24312 123.18 - 131.01: 2212 131.01 - 138.85: 112 Bond angle restraints: 50658 Sorted by residual: angle pdb=" N VAL J 63 " pdb=" CA VAL J 63 " pdb=" C VAL J 63 " ideal model delta sigma weight residual 113.71 106.15 7.56 9.50e-01 1.11e+00 6.33e+01 angle pdb=" N VAL I 63 " pdb=" CA VAL I 63 " pdb=" C VAL I 63 " ideal model delta sigma weight residual 113.71 106.17 7.54 9.50e-01 1.11e+00 6.31e+01 angle pdb=" N VAL H 63 " pdb=" CA VAL H 63 " pdb=" C VAL H 63 " ideal model delta sigma weight residual 113.71 106.18 7.53 9.50e-01 1.11e+00 6.28e+01 angle pdb=" C GLY A 891 " pdb=" N PRO A 892 " pdb=" CA PRO A 892 " ideal model delta sigma weight residual 120.14 114.12 6.02 1.06e+00 8.90e-01 3.22e+01 angle pdb=" N LEU C 517 " pdb=" CA LEU C 517 " pdb=" C LEU C 517 " ideal model delta sigma weight residual 109.24 117.77 -8.53 1.51e+00 4.39e-01 3.19e+01 ... (remaining 50653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 20140 17.56 - 35.11: 2082 35.11 - 52.67: 690 52.67 - 70.22: 261 70.22 - 87.78: 44 Dihedral angle restraints: 23217 sinusoidal: 9987 harmonic: 13230 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+01 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 -86.00 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 23214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 5892 0.305 - 0.609: 11 0.609 - 0.914: 13 0.914 - 1.218: 9 1.218 - 1.523: 9 Chirality restraints: 5934 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+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 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 ... (remaining 5931 not shown) Planarity restraints: 6495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN B 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG B1413 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN C 657 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.577 2.00e-02 2.50e+03 pdb=" C1 NAG C1413 " -0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG A1413 " 0.391 2.00e-02 2.50e+03 ... (remaining 6492 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 262 2.51 - 3.11: 25861 3.11 - 3.70: 52411 3.70 - 4.30: 78788 4.30 - 4.90: 133082 Nonbonded interactions: 290404 Sorted by model distance: nonbonded pdb=" O SER B 940 " pdb=" OG1 THR B 941 " model vdw 1.910 2.440 nonbonded pdb=" O SER C 940 " pdb=" OG1 THR C 941 " model vdw 1.910 2.440 nonbonded pdb=" O SER A 940 " pdb=" OG1 THR A 941 " model vdw 1.911 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.195 2.440 ... (remaining 290399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1146 or resid 1403 through 1414)) selection = (chain 'B' and (resid 14 through 1146 or resid 1403 through 1414)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.520 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 95.410 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.600 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.009 0.088 37230 Z= 0.571 Angle : 0.965 13.845 50658 Z= 0.548 Chirality : 0.098 1.523 5934 Planarity : 0.010 0.279 6441 Dihedral : 16.941 87.781 14568 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.41 % Favored : 90.64 % Rotamer: Outliers : 10.68 % Allowed : 15.40 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.11), residues: 4530 helix: -0.87 (0.18), residues: 741 sheet: -0.82 (0.13), residues: 1317 loop : -2.84 (0.10), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.006 0.001 HIS I 209 PHE 0.016 0.002 PHE A 133 TYR 0.022 0.002 TYR B 756 ARG 0.004 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 507 time to evaluate : 4.039 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: A 162 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7676 (p) REVERT: A 357 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7634 (tpt170) REVERT: A 389 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: A 661 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 745 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: A 796 ASP cc_start: 0.6575 (t70) cc_final: 0.6075 (p0) REVERT: A 823 PHE cc_start: 0.7445 (t80) cc_final: 0.7217 (t80) REVERT: A 913 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: A 957 GLN cc_start: 0.7786 (tt0) cc_final: 0.7436 (tm-30) REVERT: A 1010 GLN cc_start: 0.8196 (mt0) cc_final: 0.7989 (mt0) REVERT: B 66 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6019 (p-80) REVERT: B 249 LEU cc_start: 0.7043 (mt) cc_final: 0.6759 (mp) REVERT: B 305 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8177 (t) REVERT: B 373 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 505 TYR cc_start: 0.6472 (m-80) cc_final: 0.5480 (t80) REVERT: B 645 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 646 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7755 (mtp180) REVERT: B 740 MET cc_start: 0.8718 (ttt) cc_final: 0.8408 (ttm) REVERT: B 809 PRO cc_start: 0.6661 (Cg_endo) cc_final: 0.6443 (Cg_exo) REVERT: B 854 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8236 (mtpp) REVERT: B 869 MET cc_start: 0.8758 (mtt) cc_final: 0.8546 (mtt) REVERT: B 878 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8806 (mp) REVERT: B 1050 MET cc_start: 0.8702 (ptm) cc_final: 0.8449 (ptm) REVERT: C 66 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6530 (p-80) REVERT: C 188 ASN cc_start: 0.8203 (m110) cc_final: 0.7959 (m110) REVERT: C 389 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6955 (t0) REVERT: C 444 LYS cc_start: 0.7745 (pttt) cc_final: 0.7373 (ptmm) REVERT: C 469 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8206 (p) REVERT: C 516 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5685 (tm-30) REVERT: C 847 ARG cc_start: 0.5650 (ttp-110) cc_final: 0.4883 (mmt180) REVERT: H 82 MET cc_start: 0.4931 (mtm) cc_final: 0.4426 (pmm) REVERT: H 151 VAL cc_start: -0.0697 (OUTLIER) cc_final: -0.0905 (t) REVERT: H 206 ASN cc_start: -0.0037 (OUTLIER) cc_final: -0.0773 (t0) REVERT: L 18 VAL cc_start: 0.1830 (t) cc_final: 0.1352 (m) REVERT: L 169 SER cc_start: 0.2648 (OUTLIER) cc_final: 0.2331 (m) REVERT: M 46 PRO cc_start: 0.3217 (Cg_exo) cc_final: 0.2998 (Cg_endo) REVERT: M 51 SER cc_start: 0.5724 (t) cc_final: 0.5465 (p) REVERT: M 114 LYS cc_start: 0.1495 (OUTLIER) cc_final: 0.1202 (mtmt) REVERT: M 169 SER cc_start: 0.2342 (OUTLIER) cc_final: 0.1655 (m) REVERT: M 184 LEU cc_start: -0.0066 (OUTLIER) cc_final: -0.0322 (mp) REVERT: J 116 THR cc_start: 0.3755 (m) cc_final: 0.3508 (p) REVERT: N 97 ASN cc_start: 0.4793 (OUTLIER) cc_final: 0.4435 (m110) REVERT: N 99 TRP cc_start: 0.4601 (m100) cc_final: 0.4217 (m100) outliers start: 421 outliers final: 50 residues processed: 824 average time/residue: 1.1574 time to fit residues: 1199.0875 Evaluate side-chains 341 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 269 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 30.0000 chunk 343 optimal weight: 40.0000 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 355 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 411 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 239 GLN A 314 GLN A 317 ASN A 422 ASN A 450 ASN A 474 GLN A 501 ASN A 544 ASN A 564 GLN A 613 GLN A 644 GLN A 751 ASN A 804 GLN A 856 ASN A 919 ASN A 925 ASN A 935 GLN A 955 ASN A1023 ASN A1036 GLN A1054 GLN A1064 HIS A1142 GLN B 183 GLN B 239 GLN B 314 GLN B 317 ASN B 422 ASN B 450 ASN B 474 GLN B 544 ASN B 564 GLN B 613 GLN B 751 ASN B 804 GLN B 856 ASN B 913 GLN B 919 ASN B 925 ASN B 935 GLN B1023 ASN B1036 GLN B1054 GLN B1064 HIS B1142 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 173 GLN C 185 ASN C 207 HIS C 239 GLN C 314 GLN C 317 ASN C 334 ASN C 422 ASN C 450 ASN C 532 ASN C 544 ASN C 564 GLN C 751 ASN C 919 ASN C 925 ASN C 957 GLN C1023 ASN C1036 GLN C1054 GLN C1064 HIS C1142 GLN H 81 GLN H 173 HIS L 6 GLN L 40 GLN L 41 HIS L 97 ASN L 98 ASN L 192 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN M 6 GLN M 40 GLN M 98 ASN M 192 HIS M 198 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN N 6 GLN N 40 GLN N 41 HIS N 81 GLN N 192 HIS N 198 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37230 Z= 0.240 Angle : 0.722 10.003 50658 Z= 0.356 Chirality : 0.052 0.627 5934 Planarity : 0.005 0.068 6441 Dihedral : 8.958 82.758 6694 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 5.15 % Allowed : 18.47 % Favored : 76.38 % 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: -1.84 (0.12), residues: 4530 helix: 0.33 (0.19), residues: 738 sheet: -0.02 (0.15), residues: 1218 loop : -2.43 (0.10), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 36 HIS 0.006 0.001 HIS H 173 PHE 0.028 0.002 PHE L 143 TYR 0.026 0.002 TYR J 52 ARG 0.006 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 296 time to evaluate : 4.453 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 66 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6092 (p-80) REVERT: A 215 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5721 (p0) REVERT: A 309 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: A 321 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: A 386 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.6682 (mtmt) REVERT: A 465 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7283 (pt0) REVERT: A 516 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5952 (tm-30) REVERT: A 558 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8010 (mptt) REVERT: A 740 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8481 (ttt) REVERT: A 882 ILE cc_start: 0.8829 (pt) cc_final: 0.8581 (mt) REVERT: A 913 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: A 1010 GLN cc_start: 0.8257 (mt0) cc_final: 0.8040 (mt0) REVERT: A 1130 ILE cc_start: 0.8415 (mm) cc_final: 0.8201 (mp) REVERT: A 1141 LEU cc_start: 0.7939 (tt) cc_final: 0.7693 (tp) REVERT: B 52 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: B 66 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6345 (p-80) REVERT: B 169 GLU cc_start: 0.7413 (tt0) cc_final: 0.7192 (tm-30) REVERT: B 215 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6132 (t70) REVERT: B 249 LEU cc_start: 0.7403 (mt) cc_final: 0.7117 (mp) REVERT: B 298 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: B 355 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7891 (ttt180) REVERT: B 483 VAL cc_start: 0.8469 (m) cc_final: 0.8189 (p) REVERT: B 505 TYR cc_start: 0.6564 (m-80) cc_final: 0.5603 (t80) REVERT: B 572 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 604 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8152 (m) REVERT: B 645 THR cc_start: 0.8400 (m) cc_final: 0.8195 (p) REVERT: B 646 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7741 (mtp180) REVERT: B 654 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: B 740 MET cc_start: 0.8667 (ttt) cc_final: 0.8187 (ttt) REVERT: B 900 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: B 916 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 1030 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8653 (t) REVERT: B 1050 MET cc_start: 0.8780 (ptm) cc_final: 0.8443 (ptm) REVERT: C 389 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6892 (t0) REVERT: C 444 LYS cc_start: 0.7962 (pttt) cc_final: 0.7629 (ptmm) REVERT: C 516 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6191 (tm-30) REVERT: C 529 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7710 (mmtt) REVERT: C 847 ARG cc_start: 0.5740 (ttp-110) cc_final: 0.4915 (mmt180) REVERT: C 851 CYS cc_start: 0.6525 (m) cc_final: 0.6091 (m) REVERT: C 933 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7616 (mppt) REVERT: C 994 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: H 82 MET cc_start: 0.4813 (mtm) cc_final: 0.4353 (pmm) REVERT: H 179 LEU cc_start: 0.1857 (OUTLIER) cc_final: 0.1623 (tm) REVERT: M 6 GLN cc_start: 0.1161 (OUTLIER) cc_final: 0.0327 (mm-40) REVERT: M 51 SER cc_start: 0.5876 (t) cc_final: 0.5568 (p) REVERT: M 110 LEU cc_start: 0.1629 (OUTLIER) cc_final: 0.1334 (mm) REVERT: M 193 ARG cc_start: 0.2293 (OUTLIER) cc_final: 0.1908 (tpt170) REVERT: J 116 THR cc_start: 0.3984 (m) cc_final: 0.3715 (p) REVERT: N 97 ASN cc_start: 0.4779 (OUTLIER) cc_final: 0.4181 (m110) outliers start: 203 outliers final: 83 residues processed: 470 average time/residue: 1.1211 time to fit residues: 670.0551 Evaluate side-chains 351 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 238 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 118 SER Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 193 ARG Chi-restraints excluded: chain M residue 198 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 157 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 198 GLN Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 342 optimal weight: 30.0000 chunk 280 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 367 optimal weight: 50.0000 chunk 408 optimal weight: 30.0000 chunk 140 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 501 ASN A 644 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 185 ASN C 207 HIS C 607 GLN C 764 ASN C 957 GLN H 39 GLN H 173 HIS L 40 GLN L 41 HIS L 174 ASN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.134 37230 Z= 0.717 Angle : 0.998 19.533 50658 Z= 0.504 Chirality : 0.065 0.540 5934 Planarity : 0.007 0.088 6441 Dihedral : 9.530 85.120 6638 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.16 % Rotamer: Outliers : 6.39 % Allowed : 18.37 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.83 (0.12), residues: 4530 helix: -0.10 (0.19), residues: 717 sheet: -0.16 (0.14), residues: 1359 loop : -2.28 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP I 36 HIS 0.010 0.002 HIS B 69 PHE 0.035 0.004 PHE B 541 TYR 0.039 0.004 TYR H 33 ARG 0.011 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 267 time to evaluate : 3.955 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: A 52 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: A 66 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.5909 (p90) REVERT: A 137 ASN cc_start: 0.8085 (t0) cc_final: 0.7769 (t0) REVERT: A 321 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: A 386 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.6797 (mmmt) REVERT: A 389 ASP cc_start: 0.7547 (m-30) cc_final: 0.7118 (m-30) REVERT: A 440 ASN cc_start: 0.8086 (p0) cc_final: 0.7881 (p0) REVERT: A 465 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: A 493 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7241 (tp40) REVERT: A 516 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5810 (tm-30) REVERT: A 571 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7233 (t70) REVERT: A 702 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: A 921 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7875 (mptt) REVERT: B 20 THR cc_start: 0.7099 (m) cc_final: 0.6739 (p) REVERT: B 169 GLU cc_start: 0.7660 (tt0) cc_final: 0.7446 (tm-30) REVERT: B 182 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6699 (mmtm) REVERT: B 224 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 249 LEU cc_start: 0.7613 (mt) cc_final: 0.7367 (mp) REVERT: B 298 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: B 355 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7927 (ttt90) REVERT: B 389 ASP cc_start: 0.7772 (m-30) cc_final: 0.7517 (m-30) REVERT: B 421 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7202 (p90) REVERT: B 503 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7465 (m) REVERT: B 505 TYR cc_start: 0.7106 (m-80) cc_final: 0.5612 (t80) REVERT: B 567 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7333 (mtt90) REVERT: B 646 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7849 (mtp180) REVERT: B 654 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: B 900 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: B 916 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8560 (tt) REVERT: B 936 ASP cc_start: 0.7135 (t0) cc_final: 0.6899 (t0) REVERT: B 1005 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7594 (mm-40) REVERT: C 198 ASP cc_start: 0.7905 (m-30) cc_final: 0.7522 (t0) REVERT: C 421 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7153 (p90) REVERT: C 444 LYS cc_start: 0.8139 (pttt) cc_final: 0.7712 (ptmm) REVERT: C 450 ASN cc_start: 0.8096 (m-40) cc_final: 0.7773 (m-40) REVERT: C 458 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7736 (mptt) REVERT: C 516 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: C 529 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7942 (mmtm) REVERT: C 851 CYS cc_start: 0.6621 (m) cc_final: 0.6125 (m) REVERT: C 994 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: C 1091 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8117 (mtt90) REVERT: C 1092 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: H 187 LEU cc_start: 0.0223 (OUTLIER) cc_final: -0.0283 (tt) REVERT: I 186 SER cc_start: 0.0439 (OUTLIER) cc_final: 0.0179 (p) REVERT: I 202 THR cc_start: 0.2387 (OUTLIER) cc_final: 0.2022 (m) REVERT: M 6 GLN cc_start: 0.0861 (OUTLIER) cc_final: 0.0383 (mm-40) REVERT: M 49 MET cc_start: 0.5431 (tpp) cc_final: 0.5132 (mmt) REVERT: M 110 LEU cc_start: 0.2618 (OUTLIER) cc_final: 0.1662 (mm) REVERT: M 208 LYS cc_start: 0.2009 (OUTLIER) cc_final: 0.1774 (mttp) REVERT: J 116 THR cc_start: 0.4183 (m) cc_final: 0.3972 (p) REVERT: J 133 LEU cc_start: 0.1159 (OUTLIER) cc_final: 0.0831 (pp) REVERT: N 101 PHE cc_start: 0.3570 (OUTLIER) cc_final: 0.2838 (m-10) REVERT: N 193 ARG cc_start: 0.2329 (OUTLIER) cc_final: 0.1958 (mpp80) outliers start: 252 outliers final: 130 residues processed: 482 average time/residue: 1.1255 time to fit residues: 688.4418 Evaluate side-chains 396 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 232 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 118 SER Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 208 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 413 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 391 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS B 474 GLN B 935 GLN B1005 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 207 HIS C 607 GLN C 804 GLN H 173 HIS L 40 GLN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 201 HIS ** 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: 0.7626 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37230 Z= 0.196 Angle : 0.673 12.645 50658 Z= 0.338 Chirality : 0.049 0.874 5934 Planarity : 0.005 0.046 6441 Dihedral : 8.609 78.186 6624 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.50 % Rotamer: Outliers : 4.62 % Allowed : 20.17 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.34 (0.12), residues: 4530 helix: 0.71 (0.19), residues: 717 sheet: 0.17 (0.14), residues: 1311 loop : -2.07 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 99 HIS 0.005 0.001 HIS H 173 PHE 0.017 0.001 PHE I 92 TYR 0.018 0.001 TYR A 265 ARG 0.005 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 250 time to evaluate : 4.069 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: A 66 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6041 (p90) REVERT: A 137 ASN cc_start: 0.8071 (t0) cc_final: 0.7779 (t0) REVERT: A 321 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: A 421 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.5423 (p90) REVERT: A 493 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: A 558 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: A 786 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8182 (mptp) REVERT: A 841 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 900 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8007 (mtt) REVERT: A 921 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7803 (mptt) REVERT: B 20 THR cc_start: 0.7033 (m) cc_final: 0.6778 (p) REVERT: B 249 LEU cc_start: 0.7695 (mt) cc_final: 0.7493 (mp) REVERT: B 298 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: B 355 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7684 (ttt180) REVERT: B 389 ASP cc_start: 0.7621 (m-30) cc_final: 0.7362 (m-30) REVERT: B 421 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7142 (p90) REVERT: B 484 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: B 505 TYR cc_start: 0.6972 (m-80) cc_final: 0.5642 (t80) REVERT: B 646 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7777 (mtp180) REVERT: B 654 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: B 740 MET cc_start: 0.8763 (ttt) cc_final: 0.8328 (ttt) REVERT: B 900 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: B 916 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8510 (tt) REVERT: B 935 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6936 (tp-100) REVERT: B 936 ASP cc_start: 0.7020 (t0) cc_final: 0.6793 (t0) REVERT: B 1005 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: C 66 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7308 (p-80) REVERT: C 198 ASP cc_start: 0.7866 (m-30) cc_final: 0.7543 (t0) REVERT: C 444 LYS cc_start: 0.8068 (pttt) cc_final: 0.7679 (ptmm) REVERT: C 516 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6193 (tm-30) REVERT: C 529 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7877 (mmtm) REVERT: C 603 ASN cc_start: 0.6569 (t0) cc_final: 0.6132 (t0) REVERT: C 851 CYS cc_start: 0.6287 (m) cc_final: 0.5859 (m) REVERT: C 933 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7512 (mppt) REVERT: C 994 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: C 1091 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8033 (mtt90) REVERT: H 187 LEU cc_start: 0.0179 (OUTLIER) cc_final: -0.0290 (tt) REVERT: H 210 LYS cc_start: 0.1379 (OUTLIER) cc_final: 0.1174 (tttm) REVERT: L 33 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.7073 (t0) REVERT: I 186 SER cc_start: 0.0712 (OUTLIER) cc_final: 0.0395 (p) REVERT: I 202 THR cc_start: 0.2517 (OUTLIER) cc_final: 0.2150 (m) REVERT: M 110 LEU cc_start: 0.2584 (OUTLIER) cc_final: 0.1649 (mm) REVERT: N 52 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5898 (pt0) REVERT: N 159 VAL cc_start: -0.1244 (OUTLIER) cc_final: -0.1564 (t) REVERT: N 193 ARG cc_start: 0.2177 (OUTLIER) cc_final: 0.1902 (mpp80) outliers start: 182 outliers final: 94 residues processed: 401 average time/residue: 1.1705 time to fit residues: 595.6086 Evaluate side-chains 357 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 233 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 393 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A1058 HIS B 474 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN H 173 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS N 97 ASN N 112 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 37230 Z= 0.447 Angle : 0.809 18.085 50658 Z= 0.407 Chirality : 0.056 0.625 5934 Planarity : 0.006 0.064 6441 Dihedral : 8.691 69.931 6616 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 5.73 % Allowed : 19.74 % Favored : 74.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.39 (0.12), residues: 4530 helix: 0.45 (0.19), residues: 717 sheet: 0.18 (0.15), residues: 1284 loop : -2.03 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 36 HIS 0.028 0.002 HIS C 66 PHE 0.026 0.003 PHE B 541 TYR 0.027 0.003 TYR H 33 ARG 0.007 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 241 time to evaluate : 4.027 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: A 52 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: A 66 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6184 (p90) REVERT: A 137 ASN cc_start: 0.8066 (t0) cc_final: 0.7768 (t0) REVERT: A 321 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: A 389 ASP cc_start: 0.7480 (m-30) cc_final: 0.7088 (m-30) REVERT: A 421 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.5445 (p90) REVERT: A 493 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7154 (tp40) REVERT: A 702 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7345 (tp30) REVERT: A 786 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8141 (mptp) REVERT: A 841 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7806 (tt) REVERT: A 921 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7867 (mptt) REVERT: B 182 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.6741 (mmtm) REVERT: B 224 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 249 LEU cc_start: 0.7649 (mt) cc_final: 0.7421 (mp) REVERT: B 355 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7875 (ttt90) REVERT: B 389 ASP cc_start: 0.7742 (m-30) cc_final: 0.7496 (m-30) REVERT: B 421 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7293 (p90) REVERT: B 484 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6157 (mt-10) REVERT: B 505 TYR cc_start: 0.7152 (m-80) cc_final: 0.5576 (t80) REVERT: B 654 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: B 726 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9081 (mt) REVERT: B 900 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8612 (mtm) REVERT: B 916 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8536 (tt) REVERT: C 66 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7018 (p-80) REVERT: C 198 ASP cc_start: 0.7895 (m-30) cc_final: 0.7600 (t0) REVERT: C 302 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (m) REVERT: C 444 LYS cc_start: 0.8041 (pttt) cc_final: 0.7575 (ptmm) REVERT: C 458 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7703 (mptt) REVERT: C 516 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6241 (tm-30) REVERT: C 529 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7879 (mmtm) REVERT: C 661 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 851 CYS cc_start: 0.6529 (m) cc_final: 0.6089 (m) REVERT: C 983 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7666 (ptm-80) REVERT: C 994 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: H 173 HIS cc_start: 0.1496 (OUTLIER) cc_final: -0.0011 (p90) REVERT: H 187 LEU cc_start: 0.0201 (OUTLIER) cc_final: -0.0285 (tt) REVERT: I 168 LEU cc_start: 0.2213 (OUTLIER) cc_final: 0.1606 (pt) REVERT: I 186 SER cc_start: 0.0859 (OUTLIER) cc_final: 0.0537 (p) REVERT: I 202 THR cc_start: 0.2460 (OUTLIER) cc_final: 0.2079 (m) REVERT: M 110 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.1803 (mm) REVERT: M 171 GLN cc_start: 0.0714 (OUTLIER) cc_final: -0.0508 (mm-40) REVERT: M 208 LYS cc_start: 0.1974 (OUTLIER) cc_final: 0.1682 (mttm) REVERT: J 133 LEU cc_start: 0.1165 (OUTLIER) cc_final: 0.0843 (pp) REVERT: N 101 PHE cc_start: 0.3827 (OUTLIER) cc_final: 0.2771 (m-10) REVERT: N 159 VAL cc_start: -0.1295 (OUTLIER) cc_final: -0.1639 (t) REVERT: N 184 LEU cc_start: 0.0159 (OUTLIER) cc_final: -0.0488 (mp) REVERT: N 193 ARG cc_start: 0.2374 (OUTLIER) cc_final: 0.2025 (mpp80) outliers start: 226 outliers final: 125 residues processed: 432 average time/residue: 1.0834 time to fit residues: 593.8346 Evaluate side-chains 385 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 223 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 173 HIS Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 208 LYS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 0.9980 chunk 394 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 257 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 438 optimal weight: 30.0000 chunk 363 optimal weight: 0.0020 chunk 202 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 690 GLN B 474 GLN B 519 HIS B 935 GLN B 955 ASN B1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 540 ASN C 607 GLN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37230 Z= 0.156 Angle : 0.615 22.505 50658 Z= 0.307 Chirality : 0.047 0.465 5934 Planarity : 0.004 0.048 6441 Dihedral : 7.680 59.966 6610 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 3.78 % Allowed : 21.54 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.00 (0.12), residues: 4530 helix: 1.21 (0.20), residues: 714 sheet: 0.30 (0.15), residues: 1281 loop : -1.84 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 99 HIS 0.017 0.001 HIS H 173 PHE 0.024 0.001 PHE H 175 TYR 0.016 0.001 TYR B 248 ARG 0.005 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 246 time to evaluate : 4.257 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: A 66 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6182 (p90) REVERT: A 137 ASN cc_start: 0.8007 (t0) cc_final: 0.7732 (t0) REVERT: A 309 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 321 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: A 403 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.5809 (mtm-85) REVERT: A 421 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.5309 (p90) REVERT: A 493 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7202 (tp-100) REVERT: A 571 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7368 (t70) REVERT: A 786 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8116 (mptp) REVERT: A 841 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7785 (tt) REVERT: A 900 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: A 921 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7816 (mptt) REVERT: B 52 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: B 355 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7781 (ttt180) REVERT: B 389 ASP cc_start: 0.7516 (m-30) cc_final: 0.7286 (m-30) REVERT: B 421 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7289 (p90) REVERT: B 505 TYR cc_start: 0.6934 (m-80) cc_final: 0.5516 (t80) REVERT: B 654 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: B 740 MET cc_start: 0.8615 (ttt) cc_final: 0.8129 (ttt) REVERT: B 900 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8476 (mtm) REVERT: B 916 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 1005 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7742 (mm110) REVERT: B 1030 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8610 (t) REVERT: C 66 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6896 (p90) REVERT: C 78 ARG cc_start: 0.7454 (mmm160) cc_final: 0.7209 (mmt90) REVERT: C 198 ASP cc_start: 0.7790 (m-30) cc_final: 0.7550 (t0) REVERT: C 444 LYS cc_start: 0.7990 (pttt) cc_final: 0.7577 (ptmm) REVERT: C 516 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6343 (tt0) REVERT: C 529 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7808 (mmtm) REVERT: C 851 CYS cc_start: 0.6452 (m) cc_final: 0.6102 (m) REVERT: I 202 THR cc_start: 0.2394 (OUTLIER) cc_final: 0.2010 (m) REVERT: M 110 LEU cc_start: 0.2640 (OUTLIER) cc_final: 0.1565 (tp) REVERT: M 171 GLN cc_start: 0.0425 (OUTLIER) cc_final: -0.0512 (mm-40) REVERT: N 159 VAL cc_start: -0.1290 (OUTLIER) cc_final: -0.1573 (t) REVERT: N 184 LEU cc_start: 0.0193 (OUTLIER) cc_final: -0.0448 (mp) REVERT: N 193 ARG cc_start: 0.2685 (OUTLIER) cc_final: 0.2165 (mpp80) outliers start: 149 outliers final: 76 residues processed: 369 average time/residue: 1.2195 time to fit residues: 567.5931 Evaluate side-chains 334 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 233 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 368 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 436 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 266 optimal weight: 0.0000 chunk 201 optimal weight: 4.9990 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 66 HIS B 474 GLN B 519 HIS B 675 GLN B 935 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37230 Z= 0.318 Angle : 0.716 20.251 50658 Z= 0.358 Chirality : 0.051 0.385 5934 Planarity : 0.005 0.054 6441 Dihedral : 7.762 59.255 6603 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 4.49 % Allowed : 21.00 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.08 (0.12), residues: 4530 helix: 0.97 (0.19), residues: 714 sheet: 0.24 (0.14), residues: 1332 loop : -1.86 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 99 HIS 0.005 0.001 HIS A 66 PHE 0.021 0.002 PHE B 541 TYR 0.022 0.002 TYR A 265 ARG 0.007 0.001 ARG L 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 241 time to evaluate : 3.994 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: A 52 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: A 66 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6168 (p90) REVERT: A 137 ASN cc_start: 0.8022 (t0) cc_final: 0.7732 (t0) REVERT: A 321 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: A 493 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 786 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8164 (mptp) REVERT: A 841 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 900 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7975 (mtt) REVERT: A 921 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7822 (mptt) REVERT: B 182 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6708 (mmtm) REVERT: B 355 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7735 (ttt90) REVERT: B 389 ASP cc_start: 0.7694 (m-30) cc_final: 0.7424 (m-30) REVERT: B 421 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7498 (p90) REVERT: B 505 TYR cc_start: 0.7038 (m-80) cc_final: 0.5506 (t80) REVERT: B 654 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: B 661 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 726 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9091 (mt) REVERT: B 900 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8578 (mtm) REVERT: B 916 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8531 (tt) REVERT: B 935 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6878 (tp-100) REVERT: C 78 ARG cc_start: 0.7437 (mmm160) cc_final: 0.7182 (mmm160) REVERT: C 198 ASP cc_start: 0.7813 (m-30) cc_final: 0.7598 (t0) REVERT: C 444 LYS cc_start: 0.8036 (pttt) cc_final: 0.7607 (ptmm) REVERT: C 450 ASN cc_start: 0.8083 (m-40) cc_final: 0.7826 (m110) REVERT: C 516 GLU cc_start: 0.6658 (tt0) cc_final: 0.6275 (tm-30) REVERT: C 529 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7835 (mmtm) REVERT: C 661 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: C 851 CYS cc_start: 0.6444 (m) cc_final: 0.6065 (m) REVERT: C 994 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: H 187 LEU cc_start: 0.0387 (OUTLIER) cc_final: -0.0145 (tt) REVERT: M 110 LEU cc_start: 0.2713 (OUTLIER) cc_final: 0.1727 (mm) REVERT: M 171 GLN cc_start: 0.0192 (OUTLIER) cc_final: -0.0747 (mm-40) REVERT: N 101 PHE cc_start: 0.3733 (OUTLIER) cc_final: 0.2695 (m-80) REVERT: N 159 VAL cc_start: -0.1270 (OUTLIER) cc_final: -0.1563 (t) REVERT: N 184 LEU cc_start: 0.0242 (OUTLIER) cc_final: -0.0407 (mp) REVERT: N 193 ARG cc_start: 0.2537 (OUTLIER) cc_final: 0.2332 (mpp80) outliers start: 177 outliers final: 108 residues processed: 394 average time/residue: 1.1438 time to fit residues: 571.6243 Evaluate side-chains 372 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 239 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 343 optimal weight: 50.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 66 HIS B 474 GLN B 519 HIS C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 607 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37230 Z= 0.201 Angle : 0.633 16.608 50658 Z= 0.317 Chirality : 0.047 0.342 5934 Planarity : 0.004 0.055 6441 Dihedral : 7.368 59.881 6599 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 4.03 % Allowed : 21.56 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4530 helix: 1.13 (0.19), residues: 735 sheet: 0.36 (0.14), residues: 1320 loop : -1.79 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 99 HIS 0.004 0.001 HIS H 173 PHE 0.016 0.001 PHE I 92 TYR 0.027 0.001 TYR B 248 ARG 0.006 0.000 ARG L 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 250 time to evaluate : 4.158 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: A 52 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: A 66 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.5989 (p90) REVERT: A 137 ASN cc_start: 0.7979 (t0) cc_final: 0.7695 (t0) REVERT: A 321 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: A 455 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 493 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7185 (tp-100) REVERT: A 571 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7387 (t70) REVERT: A 786 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8101 (mptp) REVERT: A 841 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (tt) REVERT: A 900 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8026 (mtt) REVERT: A 921 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7793 (mptt) REVERT: B 182 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6752 (mmtm) REVERT: B 355 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7848 (ttt180) REVERT: B 389 ASP cc_start: 0.7650 (m-30) cc_final: 0.7373 (m-30) REVERT: B 421 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7498 (p90) REVERT: B 484 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6129 (mt-10) REVERT: B 505 TYR cc_start: 0.7002 (m-80) cc_final: 0.5494 (t80) REVERT: B 654 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: B 900 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8516 (mtm) REVERT: B 916 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8526 (tt) REVERT: C 444 LYS cc_start: 0.8015 (pttt) cc_final: 0.7611 (ptmm) REVERT: C 450 ASN cc_start: 0.8073 (m-40) cc_final: 0.7807 (m110) REVERT: C 516 GLU cc_start: 0.6689 (tt0) cc_final: 0.6303 (tm-30) REVERT: C 529 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7820 (mmtm) REVERT: C 661 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 759 PHE cc_start: 0.7190 (m-80) cc_final: 0.6960 (m-80) REVERT: C 851 CYS cc_start: 0.6515 (m) cc_final: 0.6141 (m) REVERT: C 994 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: H 187 LEU cc_start: 0.0357 (OUTLIER) cc_final: -0.0183 (tt) REVERT: M 49 MET cc_start: 0.5581 (tpp) cc_final: 0.5332 (ttm) REVERT: M 110 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.1750 (mm) REVERT: M 171 GLN cc_start: -0.0016 (OUTLIER) cc_final: -0.0804 (mm-40) REVERT: M 208 LYS cc_start: 0.1994 (OUTLIER) cc_final: 0.1786 (mmtp) REVERT: J 119 THR cc_start: 0.2295 (OUTLIER) cc_final: 0.1801 (m) REVERT: N 101 PHE cc_start: 0.3550 (OUTLIER) cc_final: 0.2639 (m-80) REVERT: N 159 VAL cc_start: -0.1284 (OUTLIER) cc_final: -0.1576 (t) REVERT: N 184 LEU cc_start: 0.0229 (OUTLIER) cc_final: -0.0414 (mp) REVERT: N 193 ARG cc_start: 0.2616 (OUTLIER) cc_final: 0.2260 (mpp80) outliers start: 159 outliers final: 101 residues processed: 381 average time/residue: 1.1459 time to fit residues: 551.0604 Evaluate side-chains 372 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 244 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 208 LYS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 6.9990 chunk 418 optimal weight: 30.0000 chunk 381 optimal weight: 40.0000 chunk 406 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 319 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 367 optimal weight: 3.9990 chunk 384 optimal weight: 0.6980 chunk 405 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 66 HIS B 474 GLN B 519 HIS B 935 GLN B1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 188 ASN C 607 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 81 GLN ** 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: 0.7642 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37230 Z= 0.249 Angle : 0.662 15.743 50658 Z= 0.332 Chirality : 0.049 0.325 5934 Planarity : 0.005 0.056 6441 Dihedral : 7.341 59.922 6596 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.40 % Favored : 93.47 % Rotamer: Outliers : 3.98 % Allowed : 21.56 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4530 helix: 1.05 (0.19), residues: 738 sheet: 0.37 (0.14), residues: 1320 loop : -1.79 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 99 HIS 0.004 0.001 HIS A 66 PHE 0.016 0.002 PHE B 541 TYR 0.026 0.002 TYR B 248 ARG 0.005 0.000 ARG L 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 244 time to evaluate : 4.172 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: A 52 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: A 66 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6148 (p90) REVERT: A 137 ASN cc_start: 0.7995 (t0) cc_final: 0.7708 (t0) REVERT: A 321 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 455 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7861 (tt) REVERT: A 493 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7248 (tp40) REVERT: A 571 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7400 (t70) REVERT: A 702 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: A 786 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8069 (mptp) REVERT: A 841 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7837 (tt) REVERT: A 900 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: A 921 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7810 (mptt) REVERT: B 182 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6716 (mmtm) REVERT: B 355 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7852 (ttt180) REVERT: B 389 ASP cc_start: 0.7678 (m-30) cc_final: 0.7406 (m-30) REVERT: B 421 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7636 (p90) REVERT: B 505 TYR cc_start: 0.7130 (m-80) cc_final: 0.5543 (t80) REVERT: B 654 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: B 661 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 900 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: B 916 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8527 (tt) REVERT: B 979 ASP cc_start: 0.7792 (t70) cc_final: 0.7582 (t70) REVERT: B 1005 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7629 (mm110) REVERT: C 78 ARG cc_start: 0.7124 (mmm160) cc_final: 0.6794 (mmt90) REVERT: C 444 LYS cc_start: 0.8033 (pttt) cc_final: 0.7621 (ptmm) REVERT: C 450 ASN cc_start: 0.8108 (m-40) cc_final: 0.7856 (m110) REVERT: C 516 GLU cc_start: 0.6671 (tt0) cc_final: 0.6275 (tm-30) REVERT: C 529 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7830 (mmtm) REVERT: C 661 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 851 CYS cc_start: 0.6514 (m) cc_final: 0.6171 (m) REVERT: C 994 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: C 1091 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7986 (mtt90) REVERT: H 187 LEU cc_start: 0.0359 (OUTLIER) cc_final: -0.0187 (tt) REVERT: I 179 LEU cc_start: 0.2978 (OUTLIER) cc_final: 0.2693 (tp) REVERT: M 171 GLN cc_start: 0.0388 (OUTLIER) cc_final: -0.0485 (mm-40) REVERT: M 208 LYS cc_start: 0.2072 (OUTLIER) cc_final: 0.1660 (mttm) REVERT: J 119 THR cc_start: 0.2405 (OUTLIER) cc_final: 0.1907 (m) REVERT: J 133 LEU cc_start: 0.1479 (OUTLIER) cc_final: 0.1101 (pp) REVERT: J 206 ASN cc_start: 0.1589 (OUTLIER) cc_final: 0.0979 (m-40) REVERT: N 101 PHE cc_start: 0.3586 (OUTLIER) cc_final: 0.2688 (m-80) REVERT: N 159 VAL cc_start: -0.1337 (OUTLIER) cc_final: -0.1620 (t) REVERT: N 184 LEU cc_start: 0.0330 (OUTLIER) cc_final: -0.0248 (mp) outliers start: 157 outliers final: 105 residues processed: 376 average time/residue: 1.1946 time to fit residues: 564.7707 Evaluate side-chains 375 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 240 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 144 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 208 LYS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 5.9990 chunk 430 optimal weight: 20.0000 chunk 262 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 299 optimal weight: 0.0040 chunk 451 optimal weight: 50.0000 chunk 415 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 overall best weight: 2.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 474 GLN B 519 HIS B 935 GLN B1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 607 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37230 Z= 0.275 Angle : 0.674 15.729 50658 Z= 0.339 Chirality : 0.049 0.328 5934 Planarity : 0.005 0.058 6441 Dihedral : 7.383 59.799 6596 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 3.96 % Allowed : 21.77 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.12), residues: 4530 helix: 0.98 (0.19), residues: 738 sheet: 0.37 (0.14), residues: 1338 loop : -1.78 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 99 HIS 0.005 0.001 HIS A 66 PHE 0.017 0.002 PHE I 92 TYR 0.027 0.002 TYR B 248 ARG 0.007 0.001 ARG C 847 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 240 time to evaluate : 4.454 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 52 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: A 66 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6162 (p90) REVERT: A 137 ASN cc_start: 0.7993 (t0) cc_final: 0.7714 (t0) REVERT: A 321 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: A 455 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 493 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7252 (tp40) REVERT: A 571 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7397 (t70) REVERT: A 702 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: A 740 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8503 (ttp) REVERT: A 786 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8078 (mptp) REVERT: A 841 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 900 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7994 (mtt) REVERT: A 921 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7817 (mptt) REVERT: A 1073 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8189 (tttp) REVERT: B 182 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6654 (mmtm) REVERT: B 355 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7864 (ttt180) REVERT: B 389 ASP cc_start: 0.7716 (m-30) cc_final: 0.7464 (m-30) REVERT: B 421 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7526 (p90) REVERT: B 505 TYR cc_start: 0.7162 (m-80) cc_final: 0.5571 (t80) REVERT: B 654 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: B 661 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 726 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9083 (mt) REVERT: B 900 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8598 (mtm) REVERT: B 916 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8530 (tt) REVERT: B 979 ASP cc_start: 0.7826 (t70) cc_final: 0.7586 (t70) REVERT: C 66 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.7054 (p90) REVERT: C 444 LYS cc_start: 0.8041 (pttt) cc_final: 0.7622 (ptmm) REVERT: C 450 ASN cc_start: 0.8151 (m-40) cc_final: 0.7888 (m110) REVERT: C 516 GLU cc_start: 0.6669 (tt0) cc_final: 0.6267 (tm-30) REVERT: C 529 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7838 (mmtm) REVERT: C 571 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7493 (t0) REVERT: C 661 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: C 759 PHE cc_start: 0.7315 (m-80) cc_final: 0.7059 (m-80) REVERT: C 851 CYS cc_start: 0.6433 (m) cc_final: 0.6055 (m) REVERT: C 994 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: H 187 LEU cc_start: 0.0199 (OUTLIER) cc_final: -0.0348 (tt) REVERT: M 171 GLN cc_start: 0.0394 (OUTLIER) cc_final: -0.0569 (mm-40) REVERT: M 208 LYS cc_start: 0.2266 (OUTLIER) cc_final: 0.1685 (mttm) REVERT: J 119 THR cc_start: 0.2111 (OUTLIER) cc_final: 0.1618 (m) REVERT: J 133 LEU cc_start: 0.1483 (OUTLIER) cc_final: 0.1100 (pp) REVERT: J 206 ASN cc_start: 0.1444 (OUTLIER) cc_final: 0.0873 (m-40) REVERT: N 101 PHE cc_start: 0.3572 (OUTLIER) cc_final: 0.2668 (m-80) REVERT: N 159 VAL cc_start: -0.1341 (OUTLIER) cc_final: -0.1628 (t) REVERT: N 184 LEU cc_start: 0.0372 (OUTLIER) cc_final: -0.0198 (mp) outliers start: 156 outliers final: 110 residues processed: 372 average time/residue: 1.2184 time to fit residues: 570.7208 Evaluate side-chains 382 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 239 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 208 LYS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 1.9990 chunk 382 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 369 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 474 GLN B 519 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 607 GLN C 641 ASN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133205 restraints weight = 44118.896| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 7.88 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 37230 Z= 0.422 Angle : 0.783 23.331 50658 Z= 0.394 Chirality : 0.054 0.385 5934 Planarity : 0.005 0.060 6441 Dihedral : 7.875 60.066 6595 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.69 % Rotamer: Outliers : 3.98 % Allowed : 21.71 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4530 helix: 0.67 (0.19), residues: 723 sheet: 0.23 (0.14), residues: 1350 loop : -1.88 (0.11), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 36 HIS 0.006 0.001 HIS A1064 PHE 0.027 0.003 PHE B 541 TYR 0.028 0.003 TYR B 248 ARG 0.008 0.001 ARG C 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11674.02 seconds wall clock time: 209 minutes 19.59 seconds (12559.59 seconds total)