Starting phenix.real_space_refine on Thu Feb 22 14:02:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/02_2024/7czs_30515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/02_2024/7czs_30515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/02_2024/7czs_30515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/02_2024/7czs_30515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/02_2024/7czs_30515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/02_2024/7czs_30515.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 141 5.16 5 C 21759 2.51 5 N 5619 2.21 5 O 6802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ARG 97": "NH1" <-> "NH2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34321 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "K" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "M" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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: 16.58, per 1000 atoms: 0.48 Number of scatterers: 34321 At special positions: 0 Unit cell: (146.745, 175.007, 238.053, 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 141 16.00 O 6802 8.00 N 5619 7.00 C 21759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.52 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.29 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.14 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.29 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.09 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.29 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.10 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " 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 A1406 " - " NAG A1407 " " NAG B1409 " - " NAG B1410 " " NAG C1406 " - " NAG C1407 " " 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 L 1 " - " NAG L 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 331 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " Time building additional restraints: 13.49 Conformation dependent library (CDL) restraints added in 5.9 seconds 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8030 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 76 sheets defined 18.4% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.584A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.237A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.238A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 191 No H-bonds generated for 'chain 'I' and resid 189 through 191' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.237A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.571A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.680A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.610A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.517A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.821A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.654A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.558A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.534A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.139A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 193 through 194 removed outlier: 5.992A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.888A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.118A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.863A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.605A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.530A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 152 through 156 Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.527A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG5, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'I' and resid 45 through 51 removed outlier: 6.530A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR I 33 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA I 139 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 186 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 141 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 184 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 143 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 182 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 145 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU I 180 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA I 139 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 186 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 141 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 184 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 143 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 182 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 145 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU I 180 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 152 through 156 Processing sheet with id=AH1, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AH3, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH6, first strand: chain 'J' and resid 45 through 51 removed outlier: 6.531A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AI1, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AI3, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI4, first strand: chain 'N' and resid 153 through 154 1193 hydrogen bonds defined for protein. 3183 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: 15.12 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5730 1.32 - 1.45: 10423 1.45 - 1.58: 18739 1.58 - 1.72: 3 1.72 - 1.85: 174 Bond restraints: 35069 Sorted by residual: bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.405 0.115 1.22e-02 6.72e+03 8.96e+01 bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.420 0.105 1.11e-02 8.12e+03 8.92e+01 bond pdb=" CA ASN C 30 " pdb=" C ASN C 30 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.16e-02 7.43e+03 8.16e+01 bond pdb=" CA ARG C 44 " pdb=" C ARG C 44 " ideal model delta sigma weight residual 1.521 1.414 0.107 1.24e-02 6.50e+03 7.38e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.18e-02 7.18e+03 7.29e+01 ... (remaining 35064 not shown) Histogram of bond angle deviations from ideal: 96.92 - 105.24: 832 105.24 - 113.56: 19681 113.56 - 121.88: 19854 121.88 - 130.20: 7187 130.20 - 138.52: 146 Bond angle restraints: 47700 Sorted by residual: angle pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " pdb=" CG PHE C 32 " ideal model delta sigma weight residual 113.80 103.50 10.30 1.00e+00 1.00e+00 1.06e+02 angle pdb=" CA GLN C 271 " pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 117.82 125.26 -7.44 7.80e-01 1.64e+00 9.09e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.57 7.62 8.40e-01 1.42e+00 8.23e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.62 8.98 1.00e+00 1.00e+00 8.06e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.40 -8.60 1.00e+00 1.00e+00 7.40e+01 ... (remaining 47695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 18843 17.91 - 35.83: 2124 35.83 - 53.74: 615 53.74 - 71.66: 206 71.66 - 89.57: 65 Dihedral angle restraints: 21853 sinusoidal: 9354 harmonic: 12499 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.46 -63.46 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.45 -63.45 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 21850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5582 0.328 - 0.656: 33 0.656 - 0.984: 8 0.984 - 1.312: 2 1.312 - 1.640: 3 Chirality restraints: 5628 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.62e+03 chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -3.45 1.05 2.00e-02 2.50e+03 2.73e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 5625 not shown) Planarity restraints: 6110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.243 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN B 282 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.561 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG P 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.189 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" CG ASN C 657 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.388 2.00e-02 2.50e+03 pdb=" C1 NAG C1410 " -0.291 2.00e-02 2.50e+03 ... (remaining 6107 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 431 2.51 - 3.11: 25827 3.11 - 3.71: 49612 3.71 - 4.30: 74169 4.30 - 4.90: 122995 Nonbonded interactions: 273034 Sorted by model distance: nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.914 2.440 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 1.923 2.440 nonbonded pdb=" O ASN A 334 " pdb=" ND2 ASN A 334 " model vdw 1.924 2.520 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.981 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 2.520 ... (remaining 273029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1410)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 7.230 Check model and map are aligned: 0.480 Set scattering table: 0.330 Process input model: 87.760 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 : 0.013 0.117 35069 Z= 0.818 Angle : 1.301 13.517 47700 Z= 0.782 Chirality : 0.091 1.640 5628 Planarity : 0.010 0.302 6062 Dihedral : 17.507 89.571 13673 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 35.67 Ramachandran Plot: Outliers : 4.08 % Allowed : 11.55 % Favored : 84.38 % Rotamer: Outliers : 12.67 % Allowed : 17.10 % Favored : 70.23 % Cbeta Deviations : 0.20 % 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: -4.03 (0.11), residues: 4244 helix: -2.26 (0.16), residues: 683 sheet: -1.74 (0.14), residues: 1215 loop : -3.46 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.166 0.005 TRP C 64 HIS 0.009 0.002 HIS B 207 PHE 0.119 0.005 PHE C 220 TYR 0.091 0.003 TYR C 38 ARG 0.011 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 474 poor density : 573 time to evaluate : 3.850 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8324 (mm) cc_final: 0.8075 (mt) REVERT: A 203 ILE cc_start: 0.7006 (mt) cc_final: 0.6709 (mt) REVERT: A 231 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3696 (mt) REVERT: A 438 SER cc_start: 0.1285 (OUTLIER) cc_final: 0.0151 (m) REVERT: A 537 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6708 (mtpp) REVERT: A 939 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7380 (m) REVERT: A 998 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8382 (p) REVERT: B 114 THR cc_start: 0.2564 (OUTLIER) cc_final: 0.2361 (m) REVERT: B 212 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4609 (pp) REVERT: B 214 ARG cc_start: 0.0733 (OUTLIER) cc_final: -0.0100 (ttm110) REVERT: B 459 SER cc_start: 0.4892 (OUTLIER) cc_final: 0.4583 (m) REVERT: B 517 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.4167 (pt) REVERT: B 540 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6673 (t0) REVERT: B 588 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8313 (m) REVERT: B 591 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 697 MET cc_start: 0.7834 (ptm) cc_final: 0.7565 (ptp) REVERT: B 869 MET cc_start: 0.7766 (mtt) cc_final: 0.7518 (mtt) REVERT: B 917 TYR cc_start: 0.8366 (m-80) cc_final: 0.8107 (m-80) REVERT: C 305 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6755 (t) REVERT: C 517 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5517 (mp) REVERT: C 547 THR cc_start: 0.7538 (m) cc_final: 0.7113 (p) REVERT: C 699 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 787 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: C 794 ILE cc_start: 0.7680 (mp) cc_final: 0.7437 (tt) REVERT: C 814 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6225 (ptpt) REVERT: C 904 TYR cc_start: 0.8019 (m-10) cc_final: 0.7807 (m-10) REVERT: C 917 TYR cc_start: 0.8668 (m-80) cc_final: 0.8298 (m-80) REVERT: H 33 TYR cc_start: 0.3049 (m-80) cc_final: 0.2174 (m-80) REVERT: H 82 MET cc_start: -0.1465 (ptp) cc_final: -0.2229 (ptp) REVERT: H 158 SER cc_start: 0.1954 (OUTLIER) cc_final: 0.1663 (p) REVERT: I 140 LEU cc_start: 0.0697 (OUTLIER) cc_final: 0.0127 (mp) REVERT: I 158 SER cc_start: 0.2620 (OUTLIER) cc_final: 0.2298 (m) REVERT: I 199 ASN cc_start: 0.3497 (OUTLIER) cc_final: 0.2383 (t0) REVERT: M 63 SER cc_start: 0.4912 (OUTLIER) cc_final: 0.4667 (m) REVERT: J 63 VAL cc_start: 0.0504 (OUTLIER) cc_final: 0.0121 (m) REVERT: J 100 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2700 (mt) REVERT: N 49 TYR cc_start: 0.3254 (OUTLIER) cc_final: 0.2875 (t80) REVERT: N 54 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.0629 (mp) REVERT: N 110 VAL cc_start: 0.4253 (t) cc_final: 0.3916 (m) outliers start: 474 outliers final: 83 residues processed: 969 average time/residue: 0.4538 time to fit residues: 712.7968 Evaluate side-chains 397 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 287 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 166 HIS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 202 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 0.0050 chunk 333 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 422 ASN A 440 ASN A 498 GLN A 644 GLN A 658 ASN A 690 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 969 ASN A1101 HIS ** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 115 GLN B 188 ASN B 239 GLN B 245 HIS B 422 ASN B 440 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 498 GLN B 703 ASN B 901 GLN B 913 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 949 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 30 ASN C 81 ASN C 87 ASN C 115 GLN C 125 ASN C 388 ASN C 422 ASN C 440 ASN C 493 GLN C 498 GLN C 542 ASN C 544 ASN C 641 ASN C 655 HIS C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS C1106 GLN K 90 GLN M 37 GLN N 37 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35069 Z= 0.231 Angle : 0.836 12.723 47700 Z= 0.413 Chirality : 0.054 0.777 5628 Planarity : 0.006 0.060 6062 Dihedral : 9.646 63.468 6287 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.55 % Favored : 90.81 % Rotamer: Outliers : 5.88 % Allowed : 19.91 % Favored : 74.21 % 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: -2.62 (0.12), residues: 4244 helix: -0.06 (0.19), residues: 693 sheet: -0.78 (0.14), residues: 1184 loop : -2.92 (0.11), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 105 HIS 0.008 0.001 HIS A 519 PHE 0.027 0.002 PHE C 133 TYR 0.033 0.002 TYR M 32 ARG 0.008 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 337 time to evaluate : 3.610 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: A 153 MET cc_start: 0.1288 (ptt) cc_final: -0.0157 (mmm) REVERT: B 97 LYS cc_start: 0.3489 (OUTLIER) cc_final: 0.3148 (ttmt) REVERT: B 266 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: B 869 MET cc_start: 0.7878 (mtt) cc_final: 0.7659 (mtt) REVERT: B 902 MET cc_start: 0.8985 (tpp) cc_final: 0.8438 (tpt) REVERT: C 236 THR cc_start: 0.7401 (t) cc_final: 0.7177 (m) REVERT: C 266 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5665 (m-80) REVERT: C 305 SER cc_start: 0.7572 (OUTLIER) cc_final: 0.7299 (t) REVERT: C 547 THR cc_start: 0.7836 (m) cc_final: 0.7513 (p) REVERT: C 587 ILE cc_start: 0.9147 (mt) cc_final: 0.8861 (mt) REVERT: H 50 VAL cc_start: 0.4823 (t) cc_final: 0.3361 (t) REVERT: H 82 MET cc_start: -0.1062 (ptp) cc_final: -0.1745 (ptp) REVERT: I 99 THR cc_start: -0.1179 (OUTLIER) cc_final: -0.1510 (p) REVERT: I 118 THR cc_start: 0.2921 (OUTLIER) cc_final: 0.2581 (p) REVERT: I 140 LEU cc_start: 0.0801 (OUTLIER) cc_final: 0.0335 (mp) REVERT: I 199 ASN cc_start: 0.3566 (OUTLIER) cc_final: 0.2355 (t0) REVERT: N 90 GLN cc_start: 0.0318 (pp30) cc_final: -0.0814 (mt0) REVERT: N 110 VAL cc_start: 0.4198 (t) cc_final: 0.3648 (m) outliers start: 220 outliers final: 102 residues processed: 527 average time/residue: 0.4336 time to fit residues: 382.7535 Evaluate side-chains 357 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 247 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 166 HIS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 105 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 202 SER Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 2.9990 chunk 120 optimal weight: 0.0370 chunk 321 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 387 optimal weight: 20.0000 chunk 418 optimal weight: 5.9990 chunk 345 optimal weight: 20.0000 chunk 384 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 125 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN H 81 GLN M 6 GLN M 137 ASN J 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35069 Z= 0.211 Angle : 0.734 12.991 47700 Z= 0.361 Chirality : 0.051 0.679 5628 Planarity : 0.005 0.066 6062 Dihedral : 8.306 59.950 6168 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.88 % Favored : 90.72 % Rotamer: Outliers : 5.45 % Allowed : 21.08 % Favored : 73.46 % 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: -1.98 (0.12), residues: 4244 helix: 0.72 (0.20), residues: 689 sheet: -0.37 (0.14), residues: 1209 loop : -2.60 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 105 HIS 0.007 0.001 HIS C 207 PHE 0.026 0.002 PHE H 102 TYR 0.024 0.002 TYR M 32 ARG 0.005 0.001 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 268 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0999 (ptt) cc_final: 0.0133 (mmm) REVERT: A 660 TYR cc_start: 0.8064 (m-80) cc_final: 0.7798 (m-80) REVERT: A 725 GLU cc_start: 0.7540 (tt0) cc_final: 0.7204 (tt0) REVERT: B 266 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: B 869 MET cc_start: 0.8062 (mtt) cc_final: 0.7842 (mtt) REVERT: C 266 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.5706 (m-80) REVERT: C 517 LEU cc_start: 0.5249 (OUTLIER) cc_final: 0.4228 (pt) REVERT: C 547 THR cc_start: 0.8175 (m) cc_final: 0.7857 (p) REVERT: C 587 ILE cc_start: 0.9146 (mt) cc_final: 0.8925 (mt) REVERT: C 1029 MET cc_start: 0.8266 (tpp) cc_final: 0.7620 (ttm) REVERT: H 80 LEU cc_start: 0.0211 (tt) cc_final: -0.0266 (tt) REVERT: I 99 THR cc_start: -0.0319 (OUTLIER) cc_final: -0.0523 (p) REVERT: I 118 THR cc_start: 0.2437 (OUTLIER) cc_final: 0.2082 (p) REVERT: I 140 LEU cc_start: 0.1288 (OUTLIER) cc_final: 0.0672 (mp) REVERT: I 199 ASN cc_start: 0.3223 (OUTLIER) cc_final: 0.2043 (t0) REVERT: M 33 LEU cc_start: -0.1447 (OUTLIER) cc_final: -0.2052 (mt) REVERT: N 89 GLN cc_start: 0.0158 (OUTLIER) cc_final: -0.1095 (mm-40) REVERT: N 110 VAL cc_start: 0.4542 (t) cc_final: 0.3963 (m) outliers start: 204 outliers final: 114 residues processed: 444 average time/residue: 0.4218 time to fit residues: 317.9062 Evaluate side-chains 352 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 229 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 105 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 202 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 201 optimal weight: 0.3980 chunk 42 optimal weight: 50.0000 chunk 184 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 411 optimal weight: 30.0000 chunk 203 optimal weight: 8.9990 chunk 368 optimal weight: 0.0670 chunk 110 optimal weight: 0.1980 overall best weight: 0.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 493 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 35069 Z= 0.157 Angle : 0.670 11.605 47700 Z= 0.327 Chirality : 0.049 0.606 5628 Planarity : 0.004 0.056 6062 Dihedral : 7.416 58.646 6147 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.40 % Favored : 92.30 % Rotamer: Outliers : 4.25 % Allowed : 22.69 % Favored : 73.06 % 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: -1.53 (0.12), residues: 4244 helix: 1.19 (0.21), residues: 688 sheet: -0.02 (0.15), residues: 1216 loop : -2.38 (0.11), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 105 HIS 0.005 0.001 HIS C 207 PHE 0.027 0.001 PHE H 102 TYR 0.020 0.001 TYR M 32 ARG 0.006 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 258 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1083 (ptt) cc_final: 0.0052 (mmm) REVERT: A 725 GLU cc_start: 0.7529 (tt0) cc_final: 0.7259 (tt0) REVERT: B 588 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8176 (m) REVERT: C 126 VAL cc_start: 0.6339 (t) cc_final: 0.6043 (t) REVERT: C 266 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.5649 (m-80) REVERT: C 547 THR cc_start: 0.8263 (m) cc_final: 0.8021 (p) REVERT: C 787 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: C 796 ASP cc_start: 0.6990 (t0) cc_final: 0.6627 (p0) REVERT: I 118 THR cc_start: 0.2448 (OUTLIER) cc_final: 0.2131 (p) REVERT: I 199 ASN cc_start: 0.2955 (OUTLIER) cc_final: 0.1834 (t0) REVERT: N 89 GLN cc_start: -0.0400 (OUTLIER) cc_final: -0.0987 (mm-40) REVERT: N 110 VAL cc_start: 0.4571 (t) cc_final: 0.3891 (m) outliers start: 159 outliers final: 87 residues processed: 395 average time/residue: 0.4153 time to fit residues: 283.6214 Evaluate side-chains 319 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 226 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 306 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 351 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 369 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN B 30 ASN B 87 ASN B 218 GLN B 481 ASN B 487 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 207 HIS C 804 GLN C 955 ASN C 957 GLN H 39 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN N 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 35069 Z= 0.416 Angle : 0.864 14.676 47700 Z= 0.423 Chirality : 0.055 0.699 5628 Planarity : 0.006 0.065 6062 Dihedral : 8.226 58.498 6136 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.04 % Favored : 89.66 % Rotamer: Outliers : 6.12 % Allowed : 22.31 % Favored : 71.57 % 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: -1.81 (0.12), residues: 4244 helix: 0.54 (0.20), residues: 694 sheet: -0.22 (0.14), residues: 1225 loop : -2.42 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 105 HIS 0.007 0.002 HIS A 245 PHE 0.028 0.003 PHE C 157 TYR 0.030 0.003 TYR B 904 ARG 0.014 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 234 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1345 (ptt) cc_final: 0.0654 (mmm) REVERT: A 460 ASN cc_start: 0.7413 (m-40) cc_final: 0.6581 (m-40) REVERT: A 1029 MET cc_start: 0.8436 (tpp) cc_final: 0.8101 (ttm) REVERT: A 1130 ILE cc_start: 0.8486 (pt) cc_final: 0.8130 (mt) REVERT: B 170 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.3695 (t80) REVERT: C 266 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: C 787 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: C 869 MET cc_start: 0.8494 (mtm) cc_final: 0.8200 (mtm) REVERT: C 1029 MET cc_start: 0.8302 (tpp) cc_final: 0.7878 (ttm) REVERT: H 20 LEU cc_start: 0.1899 (tt) cc_final: 0.0915 (mp) REVERT: K 20 THR cc_start: 0.3735 (OUTLIER) cc_final: 0.2971 (t) REVERT: I 34 MET cc_start: -0.0446 (mmt) cc_final: -0.0811 (mmt) REVERT: I 82 MET cc_start: -0.2351 (ptp) cc_final: -0.3222 (mmm) REVERT: I 103 ASP cc_start: 0.4711 (OUTLIER) cc_final: 0.3952 (t0) REVERT: I 118 THR cc_start: 0.2306 (OUTLIER) cc_final: 0.2040 (p) REVERT: M 141 PRO cc_start: 0.1464 (Cg_exo) cc_final: 0.1226 (Cg_endo) REVERT: N 49 TYR cc_start: 0.1930 (OUTLIER) cc_final: 0.0866 (m-10) outliers start: 229 outliers final: 136 residues processed: 434 average time/residue: 0.4324 time to fit residues: 319.5184 Evaluate side-chains 331 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 188 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 0.9990 chunk 370 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 412 optimal weight: 30.0000 chunk 342 optimal weight: 0.1980 chunk 190 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A1071 GLN B1058 HIS C 99 ASN C 957 GLN H 32 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN N 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35069 Z= 0.174 Angle : 0.674 14.331 47700 Z= 0.326 Chirality : 0.048 0.548 5628 Planarity : 0.004 0.064 6062 Dihedral : 7.290 59.572 6123 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.47 % Favored : 92.30 % Rotamer: Outliers : 3.66 % Allowed : 24.75 % Favored : 71.59 % 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: -1.40 (0.13), residues: 4244 helix: 1.21 (0.21), residues: 688 sheet: -0.07 (0.15), residues: 1239 loop : -2.20 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 105 HIS 0.003 0.001 HIS J 202 PHE 0.027 0.001 PHE B 133 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 224 time to evaluate : 3.998 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: A 153 MET cc_start: 0.1622 (ptt) cc_final: 0.0760 (mmm) REVERT: A 168 PHE cc_start: 0.4844 (t80) cc_final: 0.4410 (t80) REVERT: A 460 ASN cc_start: 0.7654 (m-40) cc_final: 0.6810 (m-40) REVERT: A 1029 MET cc_start: 0.8545 (tpp) cc_final: 0.8294 (ttm) REVERT: B 245 HIS cc_start: 0.3803 (OUTLIER) cc_final: 0.0619 (p90) REVERT: C 266 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: C 787 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7422 (mt0) REVERT: C 1029 MET cc_start: 0.8245 (tpp) cc_final: 0.7683 (ttm) REVERT: I 82 MET cc_start: -0.2942 (ptp) cc_final: -0.3651 (mmm) REVERT: I 118 THR cc_start: 0.2475 (OUTLIER) cc_final: 0.2169 (p) REVERT: N 32 TYR cc_start: 0.3039 (OUTLIER) cc_final: 0.2562 (p90) REVERT: N 49 TYR cc_start: 0.1924 (OUTLIER) cc_final: 0.0799 (m-10) outliers start: 137 outliers final: 97 residues processed: 342 average time/residue: 0.4188 time to fit residues: 246.6888 Evaluate side-chains 304 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 201 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 189 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 658 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN J 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35069 Z= 0.293 Angle : 0.724 12.036 47700 Z= 0.350 Chirality : 0.050 0.610 5628 Planarity : 0.005 0.061 6062 Dihedral : 7.518 59.106 6122 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.21 % Favored : 90.53 % Rotamer: Outliers : 4.57 % Allowed : 24.69 % Favored : 70.74 % 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: -1.42 (0.13), residues: 4244 helix: 1.05 (0.20), residues: 702 sheet: -0.14 (0.14), residues: 1265 loop : -2.16 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 105 HIS 0.005 0.001 HIS A 519 PHE 0.027 0.002 PHE B 133 TYR 0.021 0.002 TYR B1067 ARG 0.017 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 209 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: A 153 MET cc_start: 0.1744 (ptt) cc_final: 0.1109 (mmm) REVERT: A 158 ARG cc_start: 0.3989 (ttt-90) cc_final: 0.3621 (ttt-90) REVERT: A 226 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 460 ASN cc_start: 0.7626 (m-40) cc_final: 0.6736 (m-40) REVERT: A 1029 MET cc_start: 0.8592 (tpp) cc_final: 0.8306 (ttm) REVERT: B 132 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4893 (pp20) REVERT: B 245 HIS cc_start: 0.4012 (OUTLIER) cc_final: 0.0880 (p90) REVERT: B 574 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7327 (t0) REVERT: B 878 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 902 MET cc_start: 0.8794 (mmt) cc_final: 0.8521 (tpt) REVERT: C 266 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: C 787 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: C 1029 MET cc_start: 0.8305 (tpp) cc_final: 0.7937 (ttm) REVERT: I 82 MET cc_start: -0.2357 (ptp) cc_final: -0.3315 (mmm) REVERT: I 118 THR cc_start: 0.2479 (OUTLIER) cc_final: 0.2233 (p) REVERT: N 49 TYR cc_start: 0.1531 (OUTLIER) cc_final: 0.0577 (m-10) REVERT: N 89 GLN cc_start: 0.0685 (OUTLIER) cc_final: 0.0043 (mm-40) outliers start: 171 outliers final: 129 residues processed: 355 average time/residue: 0.4089 time to fit residues: 250.8912 Evaluate side-chains 326 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 187 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 245 optimal weight: 0.1980 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 322 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN J 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 35069 Z= 0.150 Angle : 0.647 10.719 47700 Z= 0.312 Chirality : 0.047 0.524 5628 Planarity : 0.004 0.061 6062 Dihedral : 7.052 59.845 6122 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.59 % Favored : 92.15 % Rotamer: Outliers : 3.39 % Allowed : 26.03 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4244 helix: 1.42 (0.21), residues: 698 sheet: 0.05 (0.15), residues: 1242 loop : -2.04 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 105 HIS 0.003 0.001 HIS J 202 PHE 0.029 0.001 PHE B 133 TYR 0.023 0.001 TYR M 32 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 216 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1657 (ptt) cc_final: 0.1259 (mmm) REVERT: A 460 ASN cc_start: 0.7687 (m-40) cc_final: 0.6815 (m-40) REVERT: A 1029 MET cc_start: 0.8573 (tpp) cc_final: 0.8302 (ttm) REVERT: B 110 LEU cc_start: 0.4287 (mp) cc_final: 0.3654 (mt) REVERT: B 132 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.4947 (pp20) REVERT: B 245 HIS cc_start: 0.4061 (OUTLIER) cc_final: 0.0615 (p90) REVERT: C 266 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: C 787 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: C 1029 MET cc_start: 0.8238 (tpp) cc_final: 0.7817 (ttm) REVERT: I 82 MET cc_start: -0.2559 (ptp) cc_final: -0.3503 (mmm) REVERT: I 118 THR cc_start: 0.2536 (OUTLIER) cc_final: 0.2218 (p) REVERT: N 49 TYR cc_start: 0.1530 (OUTLIER) cc_final: 0.0607 (m-10) REVERT: N 89 GLN cc_start: 0.0692 (OUTLIER) cc_final: 0.0106 (mm-40) outliers start: 127 outliers final: 99 residues processed: 321 average time/residue: 0.4310 time to fit residues: 240.6056 Evaluate side-chains 306 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 200 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 6.9990 chunk 393 optimal weight: 10.0000 chunk 358 optimal weight: 0.4980 chunk 382 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 381 optimal weight: 20.0000 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN B 658 ASN C 751 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 35069 Z= 0.441 Angle : 0.855 14.370 47700 Z= 0.419 Chirality : 0.054 0.701 5628 Planarity : 0.006 0.156 6062 Dihedral : 8.376 59.329 6120 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.25 % Favored : 89.49 % Rotamer: Outliers : 4.17 % Allowed : 25.52 % Favored : 70.31 % 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: -1.65 (0.12), residues: 4244 helix: 0.67 (0.19), residues: 698 sheet: -0.24 (0.14), residues: 1235 loop : -2.25 (0.12), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP J 105 HIS 0.006 0.002 HIS C1058 PHE 0.032 0.003 PHE C 157 TYR 0.025 0.002 TYR A 505 ARG 0.013 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 204 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1674 (ptt) cc_final: 0.1281 (mmm) REVERT: A 360 ASN cc_start: 0.4906 (OUTLIER) cc_final: 0.4680 (p0) REVERT: A 460 ASN cc_start: 0.7662 (m-40) cc_final: 0.6892 (m-40) REVERT: A 1029 MET cc_start: 0.8488 (tpp) cc_final: 0.8122 (ttm) REVERT: B 110 LEU cc_start: 0.4872 (mp) cc_final: 0.4326 (mt) REVERT: B 132 GLU cc_start: 0.4892 (OUTLIER) cc_final: 0.4550 (pp20) REVERT: B 245 HIS cc_start: 0.4365 (OUTLIER) cc_final: 0.1358 (p-80) REVERT: C 266 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: C 787 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: C 1029 MET cc_start: 0.8321 (tpp) cc_final: 0.8080 (ttm) REVERT: H 3 GLN cc_start: 0.6102 (mp10) cc_final: 0.5663 (tm-30) REVERT: I 82 MET cc_start: -0.3155 (ptp) cc_final: -0.4038 (mmm) REVERT: N 49 TYR cc_start: 0.1122 (OUTLIER) cc_final: 0.0230 (m-10) REVERT: N 89 GLN cc_start: 0.0970 (OUTLIER) cc_final: 0.0644 (mm-40) REVERT: N 108 ARG cc_start: 0.2066 (OUTLIER) cc_final: 0.1226 (tmt170) outliers start: 156 outliers final: 115 residues processed: 344 average time/residue: 0.4327 time to fit residues: 253.4896 Evaluate side-chains 306 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 183 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 424 optimal weight: 20.0000 chunk 390 optimal weight: 20.0000 chunk 337 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 81 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35069 Z= 0.207 Angle : 0.696 12.648 47700 Z= 0.337 Chirality : 0.049 0.580 5628 Planarity : 0.005 0.085 6062 Dihedral : 7.695 57.785 6119 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.54 % Favored : 92.22 % Rotamer: Outliers : 3.05 % Allowed : 26.56 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 4244 helix: 1.10 (0.20), residues: 707 sheet: -0.14 (0.15), residues: 1248 loop : -2.14 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 105 HIS 0.004 0.001 HIS B 655 PHE 0.029 0.002 PHE B 133 TYR 0.025 0.001 TYR B 660 ARG 0.031 0.001 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 204 time to evaluate : 4.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1938 (ptt) cc_final: 0.1667 (mmm) REVERT: A 347 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: A 360 ASN cc_start: 0.5427 (OUTLIER) cc_final: 0.5029 (p0) REVERT: A 460 ASN cc_start: 0.7712 (m-40) cc_final: 0.6958 (m-40) REVERT: A 1029 MET cc_start: 0.8542 (tpp) cc_final: 0.8258 (ttm) REVERT: B 110 LEU cc_start: 0.4420 (mp) cc_final: 0.4017 (mt) REVERT: B 132 GLU cc_start: 0.5265 (OUTLIER) cc_final: 0.4891 (pp20) REVERT: B 245 HIS cc_start: 0.4213 (OUTLIER) cc_final: 0.0974 (p-80) REVERT: B 878 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8795 (tt) REVERT: C 266 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.5976 (m-80) REVERT: C 787 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: C 1029 MET cc_start: 0.8234 (tpp) cc_final: 0.7906 (ttm) REVERT: H 3 GLN cc_start: 0.6192 (mp10) cc_final: 0.5683 (tm-30) REVERT: H 61 ASP cc_start: 0.2586 (OUTLIER) cc_final: 0.2320 (m-30) REVERT: K 86 TYR cc_start: 0.3650 (m-80) cc_final: 0.3420 (m-80) REVERT: I 82 MET cc_start: -0.3230 (ptp) cc_final: -0.4099 (mmm) REVERT: M 91 LEU cc_start: 0.2386 (OUTLIER) cc_final: 0.1868 (pp) REVERT: J 18 LEU cc_start: 0.1961 (tp) cc_final: 0.1450 (pp) REVERT: N 49 TYR cc_start: 0.1155 (OUTLIER) cc_final: 0.0396 (m-10) REVERT: N 89 GLN cc_start: 0.0867 (OUTLIER) cc_final: 0.0517 (mm-40) outliers start: 114 outliers final: 87 residues processed: 307 average time/residue: 0.4361 time to fit residues: 231.2252 Evaluate side-chains 286 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 188 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 311 optimal weight: 0.0030 chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 338 optimal weight: 40.0000 chunk 141 optimal weight: 20.0000 chunk 347 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 675 GLN A1106 GLN C 196 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN N 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.197984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.169092 restraints weight = 66618.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166865 restraints weight = 128626.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.164579 restraints weight = 113309.206| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 35069 Z= 0.155 Angle : 0.652 13.023 47700 Z= 0.314 Chirality : 0.047 0.506 5628 Planarity : 0.004 0.074 6062 Dihedral : 7.060 58.870 6119 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.94 % Favored : 91.82 % Rotamer: Outliers : 2.70 % Allowed : 26.64 % Favored : 70.66 % 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: -1.11 (0.13), residues: 4244 helix: 1.51 (0.21), residues: 699 sheet: 0.05 (0.15), residues: 1220 loop : -1.99 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 105 HIS 0.009 0.001 HIS I 166 PHE 0.021 0.001 PHE C 855 TYR 0.020 0.001 TYR M 32 ARG 0.020 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6739.80 seconds wall clock time: 124 minutes 25.59 seconds (7465.59 seconds total)