Starting phenix.real_space_refine on Thu Feb 22 19:05:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v88_31793/02_2024/7v88_31793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v88_31793/02_2024/7v88_31793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v88_31793/02_2024/7v88_31793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v88_31793/02_2024/7v88_31793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v88_31793/02_2024/7v88_31793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v88_31793/02_2024/7v88_31793.pdb" } resolution = 3.3 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= -0.001 sd= 0.047 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 166 5.16 5 C 22330 2.51 5 N 5732 2.21 5 O 6870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C PHE 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 427": "OD1" <-> "OD2" Residue "G ASP 597": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35098 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Time building chain proxies: 17.87, per 1000 atoms: 0.51 Number of scatterers: 35098 At special positions: 0 Unit cell: (139.7, 155.1, 245.3, 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 166 16.00 O 6870 8.00 N 5732 7.00 C 22330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.02 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.02 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 601 " " NAG C2003 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 901 " - " ASN F 103 " " NAG F 902 " - " ASN F 322 " " NAG G 901 " - " ASN G 90 " " NAG G 902 " - " ASN G 322 " " NAG H 1 " - " ASN A 232 " " NAG I 1 " - " ASN A 280 " " NAG J 1 " - " ASN A 329 " " NAG K 1 " - " ASN A 341 " " NAG L 1 " - " ASN A 614 " " NAG M 1 " - " ASN A 707 " " NAG N 1 " - " ASN A 715 " " NAG O 1 " - " ASN A 799 " " NAG P 1 " - " ASN A1072 " " NAG Q 1 " - " ASN A1096 " " NAG R 1 " - " ASN A1132 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 163 " " NAG U 1 " - " ASN B 280 " " NAG V 1 " - " ASN B 341 " " NAG W 1 " - " ASN B 614 " " NAG X 1 " - " ASN B 707 " " NAG Y 1 " - " ASN B 715 " " NAG Z 1 " - " ASN B 799 " " NAG a 1 " - " ASN B1072 " " NAG b 1 " - " ASN B1096 " " NAG c 1 " - " ASN B1132 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 163 " " NAG f 1 " - " ASN C 232 " " NAG g 1 " - " ASN C 280 " " NAG h 1 " - " ASN C 329 " " NAG i 1 " - " ASN C 341 " " NAG j 1 " - " ASN C 614 " " NAG k 1 " - " ASN C 707 " " NAG l 1 " - " ASN C 715 " " NAG m 1 " - " ASN C 799 " " NAG n 1 " - " ASN C1072 " " NAG o 1 " - " ASN C1096 " " NAG p 1 " - " ASN C1132 " Time building additional restraints: 14.05 Conformation dependent library (CDL) restraints added in 6.2 seconds 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8044 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 48 sheets defined 36.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.520A pdb=" N PHE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.197A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.993A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.670A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 757 through 781 removed outlier: 3.917A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.622A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.506A pdb=" N ILE A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.505A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.500A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.525A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.889A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.707A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.190A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.363A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.692A pdb=" N THR B 570 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.782A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.672A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.723A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.724A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 removed outlier: 3.541A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.531A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.650A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.986A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.615A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.403A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.029A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.816A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 500 through 503 Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 758 through 781 removed outlier: 3.505A pdb=" N ASN C 762 " --> pdb=" O CYS C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.540A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.335A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 Processing helix chain 'C' and resid 983 through 1032 removed outlier: 5.426A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.825A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.623A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.519A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.536A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.667A pdb=" N LEU F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.656A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.963A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.520A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.720A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.120A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.858A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.738A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 532 removed outlier: 3.813A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.506A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 3.532A pdb=" N SER F 563 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 560 through 564' Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.669A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.786A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 4.018A pdb=" N HIS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 80 removed outlier: 3.519A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 194 removed outlier: 3.793A pdb=" N LYS G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Proline residue: G 178 - end of helix Processing helix chain 'G' and resid 198 through 204 Processing helix chain 'G' and resid 218 through 231 removed outlier: 3.567A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 252 Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 386 Processing helix chain 'G' and resid 387 through 388 No H-bonds generated for 'chain 'G' and resid 387 through 388' Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 399 through 412 removed outlier: 3.798A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.784A pdb=" N ILE G 421 " --> pdb=" O HIS G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 447 removed outlier: 4.237A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 465 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.885A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 502 removed outlier: 3.508A pdb=" N SER G 502 " --> pdb=" O ASP G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 507 removed outlier: 3.526A pdb=" N VAL G 506 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 507 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 507' Processing helix chain 'G' and resid 513 through 532 removed outlier: 3.680A pdb=" N THR G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.680A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG G 559 " --> pdb=" O PHE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.721A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.585A pdb=" N PHE G 592 " --> pdb=" O PHE G 588 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.993A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.619A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 574 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.018A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 6.970A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.529A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.873A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N VAL A 654 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.670A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.586A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.474A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.391A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.518A pdb=" N LEU B 239 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 126 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 128 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 130 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 132 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLN B 134 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA B 161 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.256A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC4, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC5, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC6, first strand: chain 'B' and resid 563 through 564 removed outlier: 6.931A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.287A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 699 through 701 removed outlier: 7.007A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 726 removed outlier: 6.026A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.492A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.155A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.496A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.078A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.407A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 126 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 128 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 130 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C 132 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN C 134 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 161 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.963A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AD9, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.871A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.201A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.547A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.606A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 removed outlier: 4.837A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.892A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.247A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AF3, first strand: chain 'G' and resid 347 through 350 1491 hydrogen bonds defined for protein. 4158 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: 13.99 Time building geometry restraints manager: 15.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11134 1.34 - 1.46: 8944 1.46 - 1.58: 15609 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 35919 Sorted by residual: bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 35914 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.32: 570 104.32 - 111.77: 17344 111.77 - 119.23: 11947 119.23 - 126.68: 18501 126.68 - 134.14: 493 Bond angle restraints: 48855 Sorted by residual: angle pdb=" N VAL G 506 " pdb=" CA VAL G 506 " pdb=" C VAL G 506 " ideal model delta sigma weight residual 113.71 108.12 5.59 9.50e-01 1.11e+00 3.46e+01 angle pdb=" N VAL F 172 " pdb=" CA VAL F 172 " pdb=" C VAL F 172 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CB ARG F 192 " pdb=" CG ARG F 192 " pdb=" CD ARG F 192 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" C GLN C 23 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 121.80 131.27 -9.47 2.44e+00 1.68e-01 1.51e+01 angle pdb=" C TRP G 461 " pdb=" N MET G 462 " pdb=" CA MET G 462 " ideal model delta sigma weight residual 122.38 115.51 6.87 1.81e+00 3.05e-01 1.44e+01 ... (remaining 48850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 20181 17.94 - 35.89: 1842 35.89 - 53.83: 380 53.83 - 71.77: 76 71.77 - 89.72: 43 Dihedral angle restraints: 22522 sinusoidal: 10030 harmonic: 12492 Sorted by residual: dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -171.39 85.39 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -170.06 84.06 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 22519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5104 0.080 - 0.160: 562 0.160 - 0.240: 16 0.240 - 0.320: 1 0.320 - 0.400: 1 Chirality restraints: 5684 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5681 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.032 2.00e-02 2.50e+03 2.96e-02 1.10e+01 pdb=" CG ASN B1072 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.024 2.00e-02 2.50e+03 2.23e-02 6.19e+00 pdb=" CG ASN A 232 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 234 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO F 235 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " 0.029 5.00e-02 4.00e+02 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 742 2.66 - 3.22: 34513 3.22 - 3.78: 54832 3.78 - 4.34: 70687 4.34 - 4.90: 116840 Nonbonded interactions: 277614 Sorted by model distance: nonbonded pdb=" OG SER C 814 " pdb=" OE1 GLU C 817 " model vdw 2.106 2.440 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.147 2.440 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.151 2.440 nonbonded pdb=" OH TYR G 237 " pdb=" O VAL G 485 " model vdw 2.154 2.440 nonbonded pdb=" O PHE A 345 " pdb=" OH TYR A 449 " model vdw 2.154 2.440 ... (remaining 277609 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' selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.480 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 89.200 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.005 0.048 35919 Z= 0.302 Angle : 0.632 9.469 48855 Z= 0.321 Chirality : 0.046 0.400 5684 Planarity : 0.004 0.056 6209 Dihedral : 14.134 89.719 14340 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.29 (0.13), residues: 4229 helix: 1.52 (0.14), residues: 1357 sheet: 0.09 (0.18), residues: 775 loop : -1.52 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 884 HIS 0.004 0.001 HIS G 374 PHE 0.031 0.001 PHE B 904 TYR 0.020 0.001 TYR G 385 ARG 0.015 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 513 PHE cc_start: 0.8614 (m-10) cc_final: 0.8137 (m-80) REVERT: C 363 TYR cc_start: 0.9291 (m-80) cc_final: 0.8982 (m-80) REVERT: F 82 MET cc_start: 0.6586 (pmm) cc_final: 0.6168 (pmm) REVERT: F 462 MET cc_start: 0.3424 (mmt) cc_final: 0.3064 (ptt) REVERT: F 557 MET cc_start: 0.7578 (tpt) cc_final: 0.6929 (ttm) REVERT: F 579 MET cc_start: -0.0641 (mmt) cc_final: -0.3153 (tpt) REVERT: F 600 LYS cc_start: 0.3925 (tttt) cc_final: 0.3704 (tptp) REVERT: G 190 MET cc_start: 0.7884 (mpp) cc_final: 0.7665 (mpp) REVERT: G 249 MET cc_start: 0.3159 (mmt) cc_final: 0.1310 (ttp) REVERT: G 360 MET cc_start: 0.6524 (ppp) cc_final: 0.6233 (ppp) REVERT: G 455 MET cc_start: 0.8141 (tmm) cc_final: 0.7903 (tmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.4473 time to fit residues: 107.7210 Evaluate side-chains 113 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 358 optimal weight: 0.7980 chunk 322 optimal weight: 40.0000 chunk 178 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 172 optimal weight: 0.0970 chunk 333 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 247 optimal weight: 30.0000 chunk 385 optimal weight: 40.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN A 802 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 899 GLN B 917 ASN B 924 GLN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 924 GLN C 955 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35919 Z= 0.336 Angle : 0.596 9.380 48855 Z= 0.303 Chirality : 0.044 0.237 5684 Planarity : 0.004 0.054 6209 Dihedral : 7.537 58.860 6462 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 0.11 % Allowed : 6.85 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4229 helix: 1.63 (0.14), residues: 1378 sheet: 0.01 (0.18), residues: 770 loop : -1.54 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 477 HIS 0.006 0.001 HIS B1086 PHE 0.030 0.002 PHE B 904 TYR 0.028 0.001 TYR C1065 ARG 0.008 0.000 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 3.870 Fit side-chains REVERT: C 344 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8526 (tmm160) REVERT: C 363 TYR cc_start: 0.9309 (m-80) cc_final: 0.9012 (m-80) REVERT: F 82 MET cc_start: 0.6451 (pmm) cc_final: 0.6045 (pmm) REVERT: F 557 MET cc_start: 0.7778 (tpt) cc_final: 0.6972 (ttm) REVERT: G 190 MET cc_start: 0.7797 (mpp) cc_final: 0.7533 (mpp) REVERT: G 249 MET cc_start: 0.3385 (mmt) cc_final: 0.1639 (ttp) REVERT: G 455 MET cc_start: 0.8172 (tmm) cc_final: 0.7963 (tmm) REVERT: G 557 MET cc_start: 0.8480 (mpp) cc_final: 0.8216 (mpp) outliers start: 4 outliers final: 1 residues processed: 120 average time/residue: 0.4527 time to fit residues: 93.8142 Evaluate side-chains 109 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 262 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 386 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 383 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN A 899 GLN A 990 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN B 905 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 35919 Z= 0.495 Angle : 0.676 9.388 48855 Z= 0.343 Chirality : 0.047 0.233 5684 Planarity : 0.004 0.055 6209 Dihedral : 7.354 59.618 6462 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.95 % Favored : 92.95 % Rotamer: Outliers : 1.07 % Allowed : 11.53 % Favored : 87.40 % 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: -0.54 (0.13), residues: 4229 helix: 1.47 (0.14), residues: 1374 sheet: -0.31 (0.18), residues: 731 loop : -1.68 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 477 HIS 0.008 0.001 HIS A1056 PHE 0.030 0.002 PHE A1119 TYR 0.032 0.002 TYR C1065 ARG 0.009 0.001 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 5.096 Fit side-chains revert: symmetry clash REVERT: B 513 PHE cc_start: 0.8147 (m-80) cc_final: 0.7825 (m-80) REVERT: B 1037 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8521 (ptm160) REVERT: C 344 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8519 (tmm160) REVERT: C 363 TYR cc_start: 0.9394 (m-80) cc_final: 0.9040 (m-80) REVERT: C 738 MET cc_start: 0.8577 (mmm) cc_final: 0.8257 (tmm) REVERT: C 803 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8797 (mt) REVERT: F 82 MET cc_start: 0.6415 (pmm) cc_final: 0.6041 (pmm) REVERT: F 557 MET cc_start: 0.7841 (tpt) cc_final: 0.7321 (ptm) REVERT: G 249 MET cc_start: 0.3369 (mmt) cc_final: 0.1500 (ttp) REVERT: G 332 MET cc_start: 0.5558 (ppp) cc_final: 0.5251 (ppp) REVERT: G 366 MET cc_start: 0.7020 (tpp) cc_final: 0.6717 (mmm) REVERT: G 455 MET cc_start: 0.8310 (tmm) cc_final: 0.8086 (tmm) outliers start: 40 outliers final: 23 residues processed: 143 average time/residue: 0.4370 time to fit residues: 109.0052 Evaluate side-chains 128 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 382 optimal weight: 20.0000 chunk 290 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 42 optimal weight: 40.0000 chunk 184 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 410 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 367 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B 924 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35919 Z= 0.227 Angle : 0.548 9.552 48855 Z= 0.279 Chirality : 0.043 0.242 5684 Planarity : 0.004 0.056 6209 Dihedral : 6.627 59.438 6462 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 1.15 % Allowed : 13.27 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4229 helix: 1.72 (0.14), residues: 1375 sheet: -0.05 (0.18), residues: 779 loop : -1.57 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 477 HIS 0.004 0.001 HIS B1086 PHE 0.018 0.001 PHE A1119 TYR 0.021 0.001 TYR G 385 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 112 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 513 PHE cc_start: 0.8142 (m-80) cc_final: 0.7810 (m-80) REVERT: C 363 TYR cc_start: 0.9310 (m-80) cc_final: 0.8951 (m-80) REVERT: F 62 MET cc_start: 0.7152 (mmm) cc_final: 0.6944 (tpp) REVERT: F 82 MET cc_start: 0.6356 (pmm) cc_final: 0.6124 (pmm) REVERT: F 557 MET cc_start: 0.7792 (tpt) cc_final: 0.7098 (ptm) REVERT: G 249 MET cc_start: 0.3522 (mmt) cc_final: 0.1800 (ttp) REVERT: G 332 MET cc_start: 0.5266 (ppp) cc_final: 0.5005 (ppp) REVERT: G 366 MET cc_start: 0.6820 (tpp) cc_final: 0.6533 (mmm) REVERT: G 408 MET cc_start: 0.8374 (mpp) cc_final: 0.7748 (ppp) REVERT: G 455 MET cc_start: 0.8180 (tmm) cc_final: 0.7943 (tmm) REVERT: G 579 MET cc_start: 0.4411 (OUTLIER) cc_final: 0.3353 (tmm) outliers start: 43 outliers final: 20 residues processed: 153 average time/residue: 0.4105 time to fit residues: 111.0057 Evaluate side-chains 125 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 342 optimal weight: 40.0000 chunk 233 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 305 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 350 optimal weight: 30.0000 chunk 283 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 209 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35919 Z= 0.214 Angle : 0.540 12.011 48855 Z= 0.272 Chirality : 0.043 0.238 5684 Planarity : 0.004 0.055 6209 Dihedral : 6.209 58.978 6462 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 1.47 % Allowed : 14.28 % Favored : 84.26 % 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: -0.18 (0.13), residues: 4229 helix: 1.82 (0.14), residues: 1377 sheet: 0.00 (0.19), residues: 713 loop : -1.54 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 163 HIS 0.004 0.001 HIS G 374 PHE 0.018 0.001 PHE A 375 TYR 0.020 0.001 TYR G 385 ARG 0.003 0.000 ARG B 763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 110 time to evaluate : 3.923 Fit side-chains REVERT: B 513 PHE cc_start: 0.7956 (m-80) cc_final: 0.7649 (m-80) REVERT: B 894 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8774 (tp) REVERT: C 114 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7805 (p) REVERT: C 344 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8532 (tmm160) REVERT: C 363 TYR cc_start: 0.9282 (m-80) cc_final: 0.8918 (m-80) REVERT: C 738 MET cc_start: 0.8536 (mmm) cc_final: 0.8177 (mmm) REVERT: F 82 MET cc_start: 0.6336 (pmm) cc_final: 0.6106 (pmm) REVERT: F 360 MET cc_start: 0.4335 (mpp) cc_final: 0.4111 (mpp) REVERT: F 557 MET cc_start: 0.7784 (tpt) cc_final: 0.7095 (ptm) REVERT: G 249 MET cc_start: 0.3500 (mmt) cc_final: 0.1780 (ttp) REVERT: G 360 MET cc_start: 0.6569 (ppp) cc_final: 0.6184 (ppp) REVERT: G 366 MET cc_start: 0.6901 (tpp) cc_final: 0.6677 (mmm) REVERT: G 408 MET cc_start: 0.8326 (mpp) cc_final: 0.7708 (ppp) REVERT: G 455 MET cc_start: 0.8207 (tmm) cc_final: 0.7971 (tmm) REVERT: G 557 MET cc_start: 0.8354 (mpp) cc_final: 0.8122 (mpp) REVERT: G 579 MET cc_start: 0.4380 (OUTLIER) cc_final: 0.3278 (tmm) outliers start: 55 outliers final: 31 residues processed: 162 average time/residue: 0.4262 time to fit residues: 119.9771 Evaluate side-chains 140 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 138 optimal weight: 9.9990 chunk 369 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 411 optimal weight: 20.0000 chunk 341 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN C 899 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 35919 Z= 0.453 Angle : 0.649 10.481 48855 Z= 0.328 Chirality : 0.046 0.241 5684 Planarity : 0.004 0.055 6209 Dihedral : 6.445 59.822 6462 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.07 % Rotamer: Outliers : 1.78 % Allowed : 15.18 % Favored : 83.03 % 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: -0.42 (0.13), residues: 4229 helix: 1.66 (0.14), residues: 1367 sheet: -0.24 (0.19), residues: 719 loop : -1.66 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 163 HIS 0.007 0.001 HIS A1056 PHE 0.028 0.002 PHE C1119 TYR 0.029 0.001 TYR C1065 ARG 0.006 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 105 time to evaluate : 3.994 Fit side-chains REVERT: A 898 MET cc_start: 0.8532 (mtp) cc_final: 0.8294 (mtp) REVERT: B 513 PHE cc_start: 0.8037 (m-80) cc_final: 0.7720 (m-80) REVERT: B 894 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8818 (tp) REVERT: B 1037 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8593 (ptm160) REVERT: C 114 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7833 (p) REVERT: C 142 ASP cc_start: 0.4389 (OUTLIER) cc_final: 0.4083 (m-30) REVERT: C 363 TYR cc_start: 0.9315 (m-80) cc_final: 0.8934 (m-80) REVERT: C 738 MET cc_start: 0.8689 (mmm) cc_final: 0.8287 (tmm) REVERT: F 82 MET cc_start: 0.6395 (pmm) cc_final: 0.6159 (pmm) REVERT: F 360 MET cc_start: 0.4351 (mpp) cc_final: 0.4096 (mpp) REVERT: F 557 MET cc_start: 0.7827 (tpt) cc_final: 0.7118 (ptm) REVERT: G 190 MET cc_start: 0.7734 (mpp) cc_final: 0.7475 (mpp) REVERT: G 249 MET cc_start: 0.3463 (mmt) cc_final: 0.1738 (ttp) REVERT: G 360 MET cc_start: 0.6604 (ppp) cc_final: 0.6317 (ppp) REVERT: G 366 MET cc_start: 0.6978 (tpp) cc_final: 0.6769 (mmm) REVERT: G 455 MET cc_start: 0.8262 (tmm) cc_final: 0.8003 (tmm) REVERT: G 462 MET cc_start: 0.7203 (pmm) cc_final: 0.6957 (pmm) REVERT: G 557 MET cc_start: 0.8454 (mpp) cc_final: 0.8242 (mpp) REVERT: G 579 MET cc_start: 0.4454 (OUTLIER) cc_final: 0.3468 (tmm) outliers start: 67 outliers final: 45 residues processed: 169 average time/residue: 0.4195 time to fit residues: 126.1288 Evaluate side-chains 153 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 103 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 396 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 300 optimal weight: 0.9980 chunk 232 optimal weight: 0.1980 chunk 346 optimal weight: 40.0000 chunk 229 optimal weight: 1.9990 chunk 409 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B1104 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35919 Z= 0.165 Angle : 0.540 10.072 48855 Z= 0.270 Chirality : 0.043 0.243 5684 Planarity : 0.004 0.055 6209 Dihedral : 5.822 59.402 6462 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 1.39 % Allowed : 15.96 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4229 helix: 1.88 (0.14), residues: 1366 sheet: 0.09 (0.18), residues: 760 loop : -1.51 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 163 HIS 0.004 0.001 HIS G 374 PHE 0.019 0.001 PHE A 375 TYR 0.021 0.001 TYR G 385 ARG 0.003 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 3.995 Fit side-chains revert: symmetry clash REVERT: B 513 PHE cc_start: 0.8071 (m-80) cc_final: 0.7722 (m-80) REVERT: B 894 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8732 (tp) REVERT: B 1037 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8494 (ptm160) REVERT: C 114 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7747 (p) REVERT: C 142 ASP cc_start: 0.5109 (OUTLIER) cc_final: 0.4722 (m-30) REVERT: C 363 TYR cc_start: 0.9243 (m-80) cc_final: 0.8801 (m-80) REVERT: F 82 MET cc_start: 0.6377 (pmm) cc_final: 0.6136 (pmm) REVERT: F 557 MET cc_start: 0.7744 (tpt) cc_final: 0.7047 (ptm) REVERT: F 579 MET cc_start: -0.0643 (mmt) cc_final: -0.3203 (tpt) REVERT: G 249 MET cc_start: 0.3278 (mmt) cc_final: 0.1697 (ttp) REVERT: G 455 MET cc_start: 0.8220 (tmm) cc_final: 0.7893 (tmm) REVERT: G 579 MET cc_start: 0.4306 (OUTLIER) cc_final: 0.3127 (tmm) outliers start: 52 outliers final: 32 residues processed: 157 average time/residue: 0.4281 time to fit residues: 118.2864 Evaluate side-chains 140 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 253 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 260 optimal weight: 0.0870 chunk 279 optimal weight: 0.0470 chunk 202 optimal weight: 3.9990 chunk 38 optimal weight: 50.0000 chunk 321 optimal weight: 5.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35919 Z= 0.178 Angle : 0.549 14.168 48855 Z= 0.272 Chirality : 0.043 0.242 5684 Planarity : 0.004 0.055 6209 Dihedral : 5.612 59.498 6462 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 1.36 % Allowed : 16.44 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4229 helix: 1.85 (0.14), residues: 1382 sheet: 0.18 (0.18), residues: 756 loop : -1.48 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 163 HIS 0.004 0.001 HIS G 374 PHE 0.021 0.001 PHE A 375 TYR 0.020 0.001 TYR G 385 ARG 0.002 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 109 time to evaluate : 4.257 Fit side-chains revert: symmetry clash REVERT: B 894 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8751 (tp) REVERT: B 1037 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8504 (ptm160) REVERT: C 114 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7773 (p) REVERT: C 142 ASP cc_start: 0.5122 (OUTLIER) cc_final: 0.4736 (m-30) REVERT: C 344 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8534 (tmm160) REVERT: C 363 TYR cc_start: 0.9242 (m-80) cc_final: 0.8805 (m-80) REVERT: F 82 MET cc_start: 0.6353 (pmm) cc_final: 0.6112 (pmm) REVERT: F 557 MET cc_start: 0.7746 (tpt) cc_final: 0.7043 (ptm) REVERT: F 579 MET cc_start: -0.0657 (mmt) cc_final: -0.3189 (tpt) REVERT: G 249 MET cc_start: 0.3192 (mmt) cc_final: 0.1641 (ttp) REVERT: G 366 MET cc_start: 0.5889 (mmm) cc_final: 0.5568 (mmm) REVERT: G 455 MET cc_start: 0.8216 (tmm) cc_final: 0.7886 (tmm) REVERT: G 579 MET cc_start: 0.4410 (OUTLIER) cc_final: 0.3243 (tmm) outliers start: 51 outliers final: 36 residues processed: 156 average time/residue: 0.4325 time to fit residues: 117.7758 Evaluate side-chains 149 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 372 optimal weight: 30.0000 chunk 392 optimal weight: 0.0020 chunk 358 optimal weight: 9.9990 chunk 381 optimal weight: 40.0000 chunk 229 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 299 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 905 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35919 Z= 0.278 Angle : 0.587 13.259 48855 Z= 0.291 Chirality : 0.043 0.238 5684 Planarity : 0.004 0.054 6209 Dihedral : 5.704 59.937 6462 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 1.49 % Allowed : 16.22 % Favored : 82.29 % 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: -0.16 (0.13), residues: 4229 helix: 1.78 (0.14), residues: 1383 sheet: 0.04 (0.19), residues: 713 loop : -1.51 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 477 HIS 0.005 0.001 HIS B1086 PHE 0.021 0.001 PHE A1119 TYR 0.023 0.001 TYR C1065 ARG 0.004 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 108 time to evaluate : 3.928 Fit side-chains REVERT: B 894 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (tp) REVERT: B 1037 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8531 (ptm160) REVERT: C 114 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7736 (p) REVERT: C 142 ASP cc_start: 0.4554 (OUTLIER) cc_final: 0.4235 (m-30) REVERT: C 344 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8584 (tmm160) REVERT: C 363 TYR cc_start: 0.9269 (m-80) cc_final: 0.8844 (m-80) REVERT: F 82 MET cc_start: 0.6356 (pmm) cc_final: 0.6115 (pmm) REVERT: F 557 MET cc_start: 0.7820 (tpt) cc_final: 0.7083 (ptm) REVERT: F 579 MET cc_start: -0.0546 (mmt) cc_final: -0.3151 (tpt) REVERT: G 249 MET cc_start: 0.3392 (mmt) cc_final: 0.1681 (ttp) REVERT: G 455 MET cc_start: 0.8256 (tmm) cc_final: 0.7921 (tmm) REVERT: G 579 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.3347 (tmm) outliers start: 56 outliers final: 46 residues processed: 160 average time/residue: 0.4457 time to fit residues: 124.3684 Evaluate side-chains 155 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 104 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 250 optimal weight: 6.9990 chunk 403 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 423 optimal weight: 20.0000 chunk 389 optimal weight: 20.0000 chunk 337 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35919 Z= 0.403 Angle : 0.649 12.772 48855 Z= 0.325 Chirality : 0.045 0.239 5684 Planarity : 0.004 0.054 6209 Dihedral : 6.046 59.574 6462 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.86 % Favored : 93.10 % Rotamer: Outliers : 1.49 % Allowed : 16.33 % Favored : 82.18 % 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: -0.34 (0.13), residues: 4229 helix: 1.64 (0.14), residues: 1385 sheet: -0.12 (0.19), residues: 717 loop : -1.61 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 163 HIS 0.007 0.001 HIS A1056 PHE 0.026 0.002 PHE A1119 TYR 0.028 0.001 TYR C1065 ARG 0.005 0.000 ARG B1037 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 102 time to evaluate : 4.071 Fit side-chains REVERT: B 894 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8813 (tp) REVERT: B 1037 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8548 (ptm160) REVERT: C 114 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7571 (p) REVERT: C 142 ASP cc_start: 0.3796 (OUTLIER) cc_final: 0.3586 (m-30) REVERT: C 344 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8601 (tmm160) REVERT: C 363 TYR cc_start: 0.9271 (m-80) cc_final: 0.8840 (m-80) REVERT: F 62 MET cc_start: 0.6585 (mmm) cc_final: 0.6382 (tpp) REVERT: F 82 MET cc_start: 0.6366 (pmm) cc_final: 0.6123 (pmm) REVERT: F 557 MET cc_start: 0.7854 (tpt) cc_final: 0.7102 (ptm) REVERT: G 249 MET cc_start: 0.3401 (mmt) cc_final: 0.1674 (ttp) REVERT: G 366 MET cc_start: 0.5734 (mmm) cc_final: 0.5415 (mmm) REVERT: G 455 MET cc_start: 0.8306 (tmm) cc_final: 0.7955 (tmm) REVERT: G 579 MET cc_start: 0.4514 (OUTLIER) cc_final: 0.3374 (tmm) outliers start: 56 outliers final: 49 residues processed: 155 average time/residue: 0.4104 time to fit residues: 111.9421 Evaluate side-chains 156 residues out of total 3754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 102 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 267 optimal weight: 0.0970 chunk 359 optimal weight: 30.0000 chunk 103 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.109986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064028 restraints weight = 117745.192| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 5.68 r_work: 0.2852 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35919 Z= 0.192 Angle : 0.569 13.057 48855 Z= 0.282 Chirality : 0.043 0.242 5684 Planarity : 0.004 0.054 6209 Dihedral : 5.635 59.198 6462 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 1.33 % Allowed : 16.65 % Favored : 82.02 % 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: -0.11 (0.13), residues: 4229 helix: 1.81 (0.14), residues: 1382 sheet: 0.12 (0.19), residues: 753 loop : -1.50 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 163 HIS 0.004 0.001 HIS G 374 PHE 0.022 0.001 PHE A 375 TYR 0.020 0.001 TYR G 385 ARG 0.003 0.000 ARG C 903 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6639.45 seconds wall clock time: 122 minutes 49.35 seconds (7369.35 seconds total)