Starting phenix.real_space_refine on Tue Feb 20 02:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7d_30999/02_2024/7e7d_30999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7d_30999/02_2024/7e7d_30999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7d_30999/02_2024/7e7d_30999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7d_30999/02_2024/7e7d_30999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7d_30999/02_2024/7e7d_30999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7d_30999/02_2024/7e7d_30999_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16855 2.51 5 N 4301 2.21 5 O 5236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26509 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8429 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 51, 'TRANS': 1028} Chain breaks: 6 Chain: "B" Number of atoms: 8429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8429 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 51, 'TRANS': 1028} Chain breaks: 6 Chain: "C" Number of atoms: 8429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8429 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 51, 'TRANS': 1028} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 124 Unusual residues: {'ELA': 2, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'ELA': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.61, per 1000 atoms: 0.55 Number of scatterers: 26509 At special positions: 0 Unit cell: (129.353, 141.31, 175.007, 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 117 16.00 O 5236 8.00 N 4301 7.00 C 16855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A1601 " - " ASN A 343 " " NAG A1602 " - " ASN A 331 " " NAG A1603 " - " ASN A 603 " " NAG A1604 " - " ASN A 657 " " NAG A1605 " - " ASN A 17 " " NAG A1608 " - " ASN A 61 " " NAG B1602 " - " ASN B 343 " " NAG B1603 " - " ASN B 331 " " NAG B1604 " - " ASN B 603 " " NAG B1605 " - " ASN B 657 " " NAG B1606 " - " ASN B 17 " " NAG B1607 " - " ASN B 61 " " NAG C1601 " - " ASN C 343 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 603 " " NAG C1604 " - " ASN C 657 " " NAG C1605 " - " ASN C 17 " " NAG C1606 " - " ASN C 61 " " NAG C1607 " - " ASN C 616 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 122 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN B 616 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 709 " " NAG Y 1 " - " ASN B 165 " " NAG Z 1 " - " ASN B1074 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN C 282 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 122 " " NAG i 1 " - " ASN C 801 " " NAG j 1 " - " ASN C 709 " " NAG k 1 " - " ASN C 165 " " NAG l 1 " - " ASN C1074 " Time building additional restraints: 11.28 Conformation dependent library (CDL) restraints added in 5.3 seconds 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 40 sheets defined 24.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.652A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.627A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 620 through 623 No H-bonds generated for 'chain 'A' and resid 620 through 623' Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.514A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 844 through 847 No H-bonds generated for 'chain 'A' and resid 844 through 847' Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.068A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 4.278A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1142 through 1146 Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.652A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.627A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 617 through 623 Proline residue: B 621 - end of helix No H-bonds generated for 'chain 'B' and resid 617 through 623' Processing helix chain 'B' and resid 631 through 637 Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 782 removed outlier: 4.514A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 837 through 840 No H-bonds generated for 'chain 'B' and resid 837 through 840' Processing helix chain 'B' and resid 844 through 847 No H-bonds generated for 'chain 'B' and resid 844 through 847' Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.559A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 887 through 890 No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.067A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 4.278A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.652A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.626A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 617 through 623 Proline residue: C 621 - end of helix No H-bonds generated for 'chain 'C' and resid 617 through 623' Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 782 removed outlier: 4.514A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 837 through 840 No H-bonds generated for 'chain 'C' and resid 837 through 840' Processing helix chain 'C' and resid 844 through 847 No H-bonds generated for 'chain 'C' and resid 844 through 847' Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.561A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.067A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1031 removed outlier: 4.278A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1128 No H-bonds generated for 'chain 'C' and resid 1126 through 1128' Processing helix chain 'C' and resid 1142 through 1146 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.962A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.596A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.529A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= E, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.712A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.116A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.455A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.232A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.675A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.866A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.968A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.596A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.545A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= R, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.712A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 325 through 328 removed outlier: 8.302A pdb=" N ILE B 326 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.116A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.231A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.683A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.005A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AA, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 47 through 56 removed outlier: 3.596A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 168 through 170 removed outlier: 5.905A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= AE, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= AF, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.116A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AH, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.456A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.231A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.675A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.022A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AN, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.806A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) 951 hydrogen bonds defined for protein. 2664 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: 12.35 Time building geometry restraints manager: 11.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6100 1.33 - 1.47: 9351 1.47 - 1.61: 11481 1.61 - 1.76: 8 1.76 - 1.90: 136 Bond restraints: 27076 Sorted by residual: bond pdb=" CG ASN C 709 " pdb=" ND2 ASN C 709 " ideal model delta sigma weight residual 1.328 1.513 -0.185 2.10e-02 2.27e+03 7.80e+01 bond pdb=" CG ASN B 709 " pdb=" ND2 ASN B 709 " ideal model delta sigma weight residual 1.328 1.511 -0.183 2.10e-02 2.27e+03 7.57e+01 bond pdb=" CG ASN A 709 " pdb=" ND2 ASN A 709 " ideal model delta sigma weight residual 1.328 1.511 -0.183 2.10e-02 2.27e+03 7.56e+01 bond pdb=" C ELA A1606 " pdb=" OXT ELA A1606 " ideal model delta sigma weight residual 1.250 1.404 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C ELA A1607 " pdb=" OXT ELA A1607 " ideal model delta sigma weight residual 1.250 1.403 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 27071 not shown) Histogram of bond angle deviations from ideal: 96.75 - 104.20: 381 104.20 - 111.65: 12964 111.65 - 119.10: 9074 119.10 - 126.56: 14126 126.56 - 134.01: 270 Bond angle restraints: 36815 Sorted by residual: angle pdb=" N ARG C 319 " pdb=" CA ARG C 319 " pdb=" C ARG C 319 " ideal model delta sigma weight residual 111.28 120.77 -9.49 1.09e+00 8.42e-01 7.58e+01 angle pdb=" N THR A 167 " pdb=" CA THR A 167 " pdb=" C THR A 167 " ideal model delta sigma weight residual 111.36 120.48 -9.12 1.09e+00 8.42e-01 6.99e+01 angle pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" C ASN B 616 " ideal model delta sigma weight residual 109.85 96.75 13.10 1.58e+00 4.01e-01 6.87e+01 angle pdb=" N THR B 167 " pdb=" CA THR B 167 " pdb=" C THR B 167 " ideal model delta sigma weight residual 111.36 120.01 -8.65 1.09e+00 8.42e-01 6.29e+01 angle pdb=" N LYS A 835 " pdb=" CA LYS A 835 " pdb=" C LYS A 835 " ideal model delta sigma weight residual 110.10 99.09 11.01 1.49e+00 4.50e-01 5.46e+01 ... (remaining 36810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15527 17.99 - 35.98: 1227 35.98 - 53.98: 342 53.98 - 71.97: 84 71.97 - 89.96: 31 Dihedral angle restraints: 17211 sinusoidal: 7779 harmonic: 9432 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.44 87.44 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.41 78.41 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 17208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 4394 0.332 - 0.664: 17 0.664 - 0.995: 8 0.995 - 1.327: 1 1.327 - 1.659: 3 Chirality restraints: 4423 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.88e+03 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.87e+03 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.87e+03 ... (remaining 4420 not shown) Planarity restraints: 4703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG D 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1607 " -0.323 2.00e-02 2.50e+03 2.80e-01 9.83e+02 pdb=" C7 NAG B1607 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1607 " -0.132 2.00e-02 2.50e+03 pdb=" N2 NAG B1607 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1606 " -0.321 2.00e-02 2.50e+03 2.78e-01 9.68e+02 pdb=" C7 NAG C1606 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C1606 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C1606 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG C1606 " -0.117 2.00e-02 2.50e+03 ... (remaining 4700 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 914 2.69 - 3.24: 25388 3.24 - 3.80: 41777 3.80 - 4.35: 55711 4.35 - 4.90: 94091 Nonbonded interactions: 217881 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.140 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.140 2.440 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.141 2.440 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.218 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.218 2.440 ... (remaining 217876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1147 or resid 1602 through 1605)) selection = (chain 'B' and (resid 14 through 1147 or resid 1602 through 1605)) selection = (chain 'C' and (resid 14 through 1147 or resid 1602 through 1605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain '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 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.110 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 77.990 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.530 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.185 27076 Z= 0.599 Angle : 1.023 13.100 36815 Z= 0.609 Chirality : 0.090 1.659 4423 Planarity : 0.013 0.286 4652 Dihedral : 14.427 89.962 11013 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.69 % Allowed : 5.64 % Favored : 90.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 3198 helix: -1.40 (0.15), residues: 768 sheet: 0.15 (0.19), residues: 714 loop : -1.64 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 886 HIS 0.006 0.001 HIS C1048 PHE 0.019 0.002 PHE A 43 TYR 0.040 0.002 TYR B 756 ARG 0.004 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 364 time to evaluate : 3.243 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 315 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 319 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6416 (ptt-90) REVERT: A 487 ASN cc_start: 0.7045 (m110) cc_final: 0.6797 (m-40) REVERT: A 613 GLN cc_start: 0.7222 (pm20) cc_final: 0.6693 (tt0) REVERT: A 630 THR cc_start: 0.6614 (OUTLIER) cc_final: 0.5690 (p) REVERT: A 634 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7867 (ttm110) REVERT: A 814 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7930 (mmpt) REVERT: A 836 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6532 (pt0) REVERT: A 902 MET cc_start: 0.8630 (mmm) cc_final: 0.8317 (tpt) REVERT: A 1028 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8882 (mttm) REVERT: A 1029 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8761 (ttp) REVERT: B 287 ASP cc_start: 0.7918 (t0) cc_final: 0.7713 (t0) REVERT: B 319 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6351 (ptt-90) REVERT: B 487 ASN cc_start: 0.6982 (m110) cc_final: 0.6690 (m-40) REVERT: B 747 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 787 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7641 (mm-40) REVERT: B 814 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7951 (mmpt) REVERT: C 30 ASN cc_start: 0.7004 (m110) cc_final: 0.6658 (t0) REVERT: C 321 GLN cc_start: 0.7023 (mp10) cc_final: 0.6789 (mp10) REVERT: C 606 ASN cc_start: 0.8555 (m110) cc_final: 0.8066 (t0) REVERT: C 629 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7365 (mt) REVERT: C 630 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.6906 (p) REVERT: C 814 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7911 (mmpt) REVERT: C 902 MET cc_start: 0.8742 (mmm) cc_final: 0.8402 (mmm) REVERT: C 1028 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8934 (mttm) REVERT: C 1092 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8068 (mm-30) outliers start: 104 outliers final: 31 residues processed: 440 average time/residue: 0.3942 time to fit residues: 269.4011 Evaluate side-chains 236 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 7.9990 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 121 ASN A 134 GLN A 239 GLN A 481 ASN A 487 ASN A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 804 GLN A 856 ASN A 901 GLN A 926 GLN A1005 GLN B 49 HIS B 115 GLN B 121 ASN B 134 GLN B 207 HIS B 239 GLN B 314 GLN B 487 ASN B 580 GLN B 607 GLN B 764 ASN B 804 GLN B 901 GLN B 926 GLN B1005 GLN C 30 ASN C 121 ASN C 134 GLN C 211 ASN C 314 GLN C 474 GLN C 481 ASN C 487 ASN C 493 GLN C 498 GLN C 580 GLN C 606 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 804 GLN C 901 GLN C 926 GLN C1005 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27076 Z= 0.193 Angle : 0.586 9.739 36815 Z= 0.297 Chirality : 0.046 0.415 4423 Planarity : 0.004 0.049 4652 Dihedral : 8.818 79.229 5340 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.20 % Allowed : 9.12 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3198 helix: 0.57 (0.18), residues: 756 sheet: 0.52 (0.19), residues: 711 loop : -1.35 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 886 HIS 0.016 0.001 HIS B 207 PHE 0.014 0.001 PHE C 318 TYR 0.016 0.001 TYR B 756 ARG 0.006 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6208 (p0) cc_final: 0.5879 (p0) REVERT: A 144 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: A 489 TYR cc_start: 0.8553 (m-80) cc_final: 0.7816 (m-80) REVERT: A 613 GLN cc_start: 0.7171 (pm20) cc_final: 0.6767 (tt0) REVERT: A 814 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7949 (mmpt) REVERT: A 1028 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8852 (mttm) REVERT: B 144 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: B 489 TYR cc_start: 0.8529 (m-80) cc_final: 0.7887 (m-80) REVERT: B 814 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7853 (mmpt) REVERT: B 902 MET cc_start: 0.8456 (tpt) cc_final: 0.8228 (tpt) REVERT: C 30 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6750 (t0) REVERT: C 81 ASN cc_start: 0.6184 (p0) cc_final: 0.5896 (p0) REVERT: C 287 ASP cc_start: 0.7984 (t0) cc_final: 0.7738 (t0) REVERT: C 487 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7261 (t0) REVERT: C 529 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7538 (mmtt) REVERT: C 606 ASN cc_start: 0.8389 (m-40) cc_final: 0.7951 (t0) REVERT: C 814 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7892 (mmpt) REVERT: C 878 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8099 (mm) outliers start: 62 outliers final: 27 residues processed: 281 average time/residue: 0.3700 time to fit residues: 168.8157 Evaluate side-chains 211 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27076 Z= 0.288 Angle : 0.594 15.400 36815 Z= 0.299 Chirality : 0.046 0.338 4423 Planarity : 0.004 0.046 4652 Dihedral : 8.002 74.092 5277 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.59 % Allowed : 10.19 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3198 helix: 0.96 (0.19), residues: 777 sheet: 0.52 (0.19), residues: 723 loop : -1.28 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS A 69 PHE 0.019 0.001 PHE C 306 TYR 0.025 0.001 TYR B 756 ARG 0.004 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 191 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6258 (p0) cc_final: 0.5920 (p0) REVERT: A 287 ASP cc_start: 0.7810 (t0) cc_final: 0.7586 (t0) REVERT: A 489 TYR cc_start: 0.8590 (m-80) cc_final: 0.7868 (m-80) REVERT: A 814 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7934 (mmpt) REVERT: A 1028 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8773 (mttm) REVERT: B 138 ASP cc_start: 0.8132 (m-30) cc_final: 0.7932 (m-30) REVERT: B 613 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: B 814 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7856 (mmpt) REVERT: B 1145 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7183 (mt) REVERT: C 30 ASN cc_start: 0.7140 (m-40) cc_final: 0.6781 (t0) REVERT: C 81 ASN cc_start: 0.6262 (p0) cc_final: 0.5972 (p0) REVERT: C 287 ASP cc_start: 0.8198 (t0) cc_final: 0.7620 (t0) REVERT: C 487 ASN cc_start: 0.7669 (t0) cc_final: 0.7412 (t0) REVERT: C 606 ASN cc_start: 0.8349 (m-40) cc_final: 0.7915 (t0) REVERT: C 613 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: C 614 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: C 814 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7907 (mmpt) REVERT: C 878 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8276 (mm) outliers start: 73 outliers final: 49 residues processed: 253 average time/residue: 0.3399 time to fit residues: 144.6726 Evaluate side-chains 209 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 154 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 1.9990 chunk 221 optimal weight: 0.0050 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 280 ASN C 211 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27076 Z= 0.178 Angle : 0.526 10.497 36815 Z= 0.264 Chirality : 0.044 0.297 4423 Planarity : 0.003 0.034 4652 Dihedral : 7.595 70.752 5274 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.48 % Allowed : 11.40 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3198 helix: 1.46 (0.19), residues: 756 sheet: 0.59 (0.19), residues: 732 loop : -1.10 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS A 69 PHE 0.011 0.001 PHE C 306 TYR 0.015 0.001 TYR B 756 ARG 0.003 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 178 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6120 (p0) cc_final: 0.5791 (p0) REVERT: A 489 TYR cc_start: 0.8609 (m-80) cc_final: 0.7878 (m-80) REVERT: A 606 ASN cc_start: 0.8351 (m-40) cc_final: 0.7256 (t0) REVERT: A 613 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: A 814 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7891 (mmpt) REVERT: A 1028 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8776 (mttm) REVERT: B 582 LEU cc_start: 0.7741 (mm) cc_final: 0.7051 (tp) REVERT: B 814 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7875 (mmpt) REVERT: B 1145 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7039 (mp) REVERT: C 81 ASN cc_start: 0.6160 (p0) cc_final: 0.5940 (p0) REVERT: C 287 ASP cc_start: 0.8205 (t0) cc_final: 0.7737 (t0) REVERT: C 606 ASN cc_start: 0.8289 (m-40) cc_final: 0.7838 (t0) REVERT: C 613 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: C 614 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.6202 (m-30) REVERT: C 814 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7889 (mmpt) REVERT: C 988 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7890 (mt-10) outliers start: 70 outliers final: 41 residues processed: 234 average time/residue: 0.3335 time to fit residues: 132.9788 Evaluate side-chains 203 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 157 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 121 ASN B 115 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 27076 Z= 0.614 Angle : 0.740 11.935 36815 Z= 0.371 Chirality : 0.052 0.348 4423 Planarity : 0.005 0.044 4652 Dihedral : 8.190 76.378 5273 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.88 % Allowed : 12.07 % Favored : 85.06 % 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: -0.76 (0.14), residues: 3198 helix: 0.85 (0.19), residues: 759 sheet: 0.04 (0.18), residues: 771 loop : -1.44 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 886 HIS 0.006 0.002 HIS A 49 PHE 0.024 0.002 PHE C 133 TYR 0.043 0.002 TYR C 756 ARG 0.007 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 168 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6214 (p0) cc_final: 0.5946 (p0) REVERT: A 287 ASP cc_start: 0.7946 (t0) cc_final: 0.7681 (t0) REVERT: A 556 ASN cc_start: 0.6815 (t0) cc_final: 0.6614 (t0) REVERT: A 606 ASN cc_start: 0.8577 (m-40) cc_final: 0.7758 (t0) REVERT: A 613 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: A 814 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7779 (mmpt) REVERT: B 30 ASN cc_start: 0.7352 (m-40) cc_final: 0.6958 (t0) REVERT: B 88 ASP cc_start: 0.7885 (p0) cc_final: 0.7666 (p0) REVERT: B 814 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7821 (mmpt) REVERT: C 287 ASP cc_start: 0.8261 (t0) cc_final: 0.7815 (t0) REVERT: C 489 TYR cc_start: 0.8677 (m-80) cc_final: 0.8459 (m-80) REVERT: C 606 ASN cc_start: 0.8525 (m-40) cc_final: 0.8126 (t0) REVERT: C 614 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: C 814 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7901 (mmpt) REVERT: C 988 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7831 (mt-10) outliers start: 81 outliers final: 58 residues processed: 235 average time/residue: 0.3639 time to fit residues: 142.8108 Evaluate side-chains 213 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 153 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 1.9990 chunk 282 optimal weight: 0.0270 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 chunk 313 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN B 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27076 Z= 0.155 Angle : 0.532 10.373 36815 Z= 0.268 Chirality : 0.044 0.290 4423 Planarity : 0.004 0.037 4652 Dihedral : 7.511 71.707 5272 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.99 % Allowed : 12.99 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3198 helix: 1.57 (0.20), residues: 738 sheet: 0.40 (0.19), residues: 732 loop : -1.15 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.008 0.001 HIS A 49 PHE 0.010 0.001 PHE B 318 TYR 0.016 0.001 TYR B1067 ARG 0.002 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6063 (p0) cc_final: 0.5830 (p0) REVERT: A 287 ASP cc_start: 0.7900 (t0) cc_final: 0.7584 (t0) REVERT: A 606 ASN cc_start: 0.8375 (m-40) cc_final: 0.7436 (t0) REVERT: A 613 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: A 814 LYS cc_start: 0.8453 (mtpt) cc_final: 0.7832 (mmpt) REVERT: B 88 ASP cc_start: 0.7710 (p0) cc_final: 0.7498 (p0) REVERT: B 582 LEU cc_start: 0.7841 (mm) cc_final: 0.7163 (tp) REVERT: B 606 ASN cc_start: 0.8459 (m-40) cc_final: 0.7359 (t0) REVERT: B 814 LYS cc_start: 0.8416 (mtpt) cc_final: 0.7805 (mmpt) REVERT: C 30 ASN cc_start: 0.7239 (m-40) cc_final: 0.6877 (t0) REVERT: C 287 ASP cc_start: 0.8200 (t0) cc_final: 0.7751 (t0) REVERT: C 606 ASN cc_start: 0.8398 (m-40) cc_final: 0.7975 (t0) REVERT: C 614 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6333 (m-30) REVERT: C 878 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 988 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 1092 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8018 (mm-30) outliers start: 56 outliers final: 39 residues processed: 213 average time/residue: 0.3372 time to fit residues: 122.3795 Evaluate side-chains 198 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 190 optimal weight: 0.1980 chunk 144 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27076 Z= 0.211 Angle : 0.540 16.988 36815 Z= 0.271 Chirality : 0.045 0.289 4423 Planarity : 0.004 0.037 4652 Dihedral : 7.233 66.544 5266 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.95 % Allowed : 13.74 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3198 helix: 1.58 (0.20), residues: 759 sheet: 0.42 (0.18), residues: 774 loop : -1.11 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.007 0.001 HIS A 49 PHE 0.015 0.001 PHE C 133 TYR 0.018 0.001 TYR B 756 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6031 (p0) cc_final: 0.5792 (p0) REVERT: A 287 ASP cc_start: 0.7964 (t0) cc_final: 0.7649 (t0) REVERT: A 606 ASN cc_start: 0.8378 (m-40) cc_final: 0.7302 (t0) REVERT: A 613 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: A 814 LYS cc_start: 0.8472 (mtpt) cc_final: 0.7855 (mmpt) REVERT: B 582 LEU cc_start: 0.8012 (mm) cc_final: 0.7204 (tp) REVERT: B 606 ASN cc_start: 0.8446 (m-40) cc_final: 0.7390 (t0) REVERT: B 814 LYS cc_start: 0.8456 (mtpt) cc_final: 0.7852 (mmpt) REVERT: C 81 ASN cc_start: 0.5772 (p0) cc_final: 0.5469 (p0) REVERT: C 287 ASP cc_start: 0.8212 (t0) cc_final: 0.7752 (t0) REVERT: C 606 ASN cc_start: 0.8393 (m-40) cc_final: 0.7972 (t0) REVERT: C 614 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6374 (m-30) REVERT: C 988 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7804 (mt-10) outliers start: 55 outliers final: 43 residues processed: 216 average time/residue: 0.3497 time to fit residues: 127.6264 Evaluate side-chains 202 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27076 Z= 0.172 Angle : 0.514 13.085 36815 Z= 0.259 Chirality : 0.044 0.278 4423 Planarity : 0.004 0.051 4652 Dihedral : 7.018 60.776 5266 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.20 % Allowed : 14.09 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3198 helix: 1.69 (0.20), residues: 759 sheet: 0.47 (0.19), residues: 774 loop : -1.05 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS B 69 PHE 0.020 0.001 PHE C 759 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 173 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7929 (t0) cc_final: 0.7601 (t0) REVERT: A 606 ASN cc_start: 0.8337 (m-40) cc_final: 0.7283 (t0) REVERT: A 613 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: A 814 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7842 (mmpt) REVERT: B 582 LEU cc_start: 0.8008 (mm) cc_final: 0.7182 (tp) REVERT: B 606 ASN cc_start: 0.8429 (m-40) cc_final: 0.7399 (t0) REVERT: B 814 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7850 (mmpt) REVERT: C 287 ASP cc_start: 0.8209 (t0) cc_final: 0.7767 (t0) REVERT: C 606 ASN cc_start: 0.8362 (m-40) cc_final: 0.7952 (t0) REVERT: C 614 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: C 988 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7809 (mt-10) outliers start: 62 outliers final: 47 residues processed: 219 average time/residue: 0.3573 time to fit residues: 129.9719 Evaluate side-chains 206 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.9990 chunk 299 optimal weight: 0.0050 chunk 272 optimal weight: 0.9980 chunk 291 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 275 optimal weight: 4.9990 chunk 289 optimal weight: 0.2980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27076 Z= 0.141 Angle : 0.501 11.409 36815 Z= 0.253 Chirality : 0.044 0.269 4423 Planarity : 0.004 0.043 4652 Dihedral : 6.801 58.536 5266 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.63 % Allowed : 14.66 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3198 helix: 1.84 (0.20), residues: 759 sheet: 0.63 (0.19), residues: 726 loop : -0.91 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS A 66 PHE 0.022 0.001 PHE B 759 TYR 0.028 0.001 TYR A 266 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.8574 (m-80) cc_final: 0.7905 (m-80) REVERT: A 606 ASN cc_start: 0.8352 (m-40) cc_final: 0.7391 (t0) REVERT: A 814 LYS cc_start: 0.8463 (mtpt) cc_final: 0.7864 (mmpt) REVERT: A 837 TYR cc_start: 0.6211 (t80) cc_final: 0.5935 (t80) REVERT: B 582 LEU cc_start: 0.7972 (mm) cc_final: 0.7183 (tp) REVERT: B 606 ASN cc_start: 0.8414 (m-40) cc_final: 0.7343 (t0) REVERT: B 814 LYS cc_start: 0.8448 (mtpt) cc_final: 0.7926 (mmpt) REVERT: C 81 ASN cc_start: 0.5830 (p0) cc_final: 0.5547 (p0) REVERT: C 287 ASP cc_start: 0.8209 (t0) cc_final: 0.7795 (t0) REVERT: C 314 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 489 TYR cc_start: 0.8524 (m-80) cc_final: 0.7912 (m-80) REVERT: C 606 ASN cc_start: 0.8313 (m-40) cc_final: 0.7873 (t0) REVERT: C 613 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: C 614 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.6303 (m-30) REVERT: C 988 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7842 (mt-10) outliers start: 46 outliers final: 40 residues processed: 206 average time/residue: 0.3414 time to fit residues: 123.1973 Evaluate side-chains 206 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 187 optimal weight: 0.0370 chunk 145 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 257 optimal weight: 0.0870 chunk 26 optimal weight: 7.9990 chunk 198 optimal weight: 0.2980 chunk 157 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27076 Z= 0.153 Angle : 0.496 9.964 36815 Z= 0.251 Chirality : 0.043 0.272 4423 Planarity : 0.003 0.039 4652 Dihedral : 6.700 59.324 5266 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.77 % Allowed : 14.66 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3198 helix: 1.91 (0.20), residues: 756 sheet: 0.66 (0.19), residues: 720 loop : -0.88 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.000 HIS A 49 PHE 0.020 0.001 PHE A 759 TYR 0.016 0.001 TYR A 266 ARG 0.004 0.000 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.8559 (m-80) cc_final: 0.7902 (m-80) REVERT: A 606 ASN cc_start: 0.8333 (m-40) cc_final: 0.7327 (t0) REVERT: A 814 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7876 (mmpt) REVERT: A 837 TYR cc_start: 0.6237 (t80) cc_final: 0.5957 (t80) REVERT: A 1031 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: B 582 LEU cc_start: 0.7914 (mm) cc_final: 0.7142 (tp) REVERT: B 606 ASN cc_start: 0.8388 (m-40) cc_final: 0.7349 (t0) REVERT: B 814 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7933 (mmpt) REVERT: C 81 ASN cc_start: 0.5816 (p0) cc_final: 0.5531 (p0) REVERT: C 287 ASP cc_start: 0.8169 (t0) cc_final: 0.7698 (t0) REVERT: C 314 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8503 (mm-40) REVERT: C 489 TYR cc_start: 0.8506 (m-80) cc_final: 0.7926 (m-80) REVERT: C 606 ASN cc_start: 0.8342 (m-40) cc_final: 0.7917 (t0) REVERT: C 613 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: C 614 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6242 (m-30) REVERT: C 988 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7821 (mt-10) outliers start: 50 outliers final: 43 residues processed: 208 average time/residue: 0.3325 time to fit residues: 119.0830 Evaluate side-chains 206 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 264 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN C 30 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097867 restraints weight = 40505.723| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.63 r_work: 0.3114 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27076 Z= 0.166 Angle : 0.497 8.990 36815 Z= 0.251 Chirality : 0.043 0.271 4423 Planarity : 0.003 0.038 4652 Dihedral : 6.624 59.876 5266 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 14.59 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3198 helix: 1.97 (0.20), residues: 744 sheet: 0.73 (0.19), residues: 702 loop : -0.92 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.000 HIS A 49 PHE 0.010 0.001 PHE B 318 TYR 0.015 0.001 TYR C1067 ARG 0.004 0.000 ARG B1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5264.54 seconds wall clock time: 97 minutes 37.55 seconds (5857.55 seconds total)