Starting phenix.real_space_refine on Sun Mar 17 13:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpn_23480/03_2024/7lpn_23480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpn_23480/03_2024/7lpn_23480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpn_23480/03_2024/7lpn_23480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpn_23480/03_2024/7lpn_23480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpn_23480/03_2024/7lpn_23480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpn_23480/03_2024/7lpn_23480.pdb" } resolution = 3.61 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= 0.016 sd= 0.107 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 123 5.16 5 C 11094 2.51 5 N 2961 2.21 5 O 3609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 589": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 584": "OE1" <-> "OE2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17787 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.95, per 1000 atoms: 0.56 Number of scatterers: 17787 At special positions: 0 Unit cell: (130.442, 132.563, 120.897, 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 123 16.00 O 3609 8.00 N 2961 7.00 C 11094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA a 3 " - " MAN a 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 j 2 " - " BMA j 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 137 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 363 " " NAG C 609 " - " ASN C 160 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 276 " " NAG F 604 " - " ASN F 339 " " NAG F 605 " - " ASN F 355 " " NAG F 606 " - " ASN F 137 " " NAG F 607 " - " ASN F 448 " " NAG F 608 " - " ASN F 363 " " NAG F 609 " - " ASN F 160 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 137 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 363 " " NAG G 609 " - " ASN G 160 " " NAG J 1 " - " ASN G 156 " " NAG K 1 " - " ASN G 197 " " NAG L 1 " - " ASN G 234 " " NAG M 1 " - " ASN G 295 " " NAG N 1 " - " ASN G 301 " " NAG O 1 " - " ASN G 332 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 392 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 234 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 386 " " NAG Z 1 " - " ASN C 392 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 234 " " NAG e 1 " - " ASN F 295 " " NAG f 1 " - " ASN F 301 " " NAG g 1 " - " ASN F 332 " " NAG h 1 " - " ASN F 386 " " NAG i 1 " - " ASN F 392 " " NAG j 1 " - " ASN F 262 " Time building additional restraints: 8.76 Conformation dependent library (CDL) restraints added in 3.2 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3852 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 36 sheets defined 21.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.643A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.877A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.003A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.645A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 641 through 661 removed outlier: 3.654A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.552A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.733A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100C through 100E No H-bonds generated for 'chain 'H' and resid 100C through 100E' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.686A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.960A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.587A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.668A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.587A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.188A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.671A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.218A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.710A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.184A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.970A pdb=" N GLN D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 100C through 100E No H-bonds generated for 'chain 'D' and resid 100C through 100E' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 538 through 543 removed outlier: 3.828A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.148A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.544A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 637 removed outlier: 3.644A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 661 Processing helix chain 'F' and resid 99 through 115 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.669A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 481 removed outlier: 4.085A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.701A pdb=" N GLN I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 100C through 100E No H-bonds generated for 'chain 'I' and resid 100C through 100E' Processing sheet with id=AA1, first strand: chain 'B' and resid 604 through 609 removed outlier: 3.525A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.693A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.729A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.777A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.777A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.061A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 34 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.061A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.861A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.230A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.656A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.683A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.415A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.000A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.520A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 360 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.674A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.502A pdb=" N VAL D 5 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR D 110 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 34 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR D 110 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 604 through 609 removed outlier: 3.511A pdb=" N CYS E 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL F 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.744A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.710A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AD2, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.548A pdb=" N ARG F 273 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.548A pdb=" N ARG F 273 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.691A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.503A pdb=" N VAL I 5 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.775A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET I 34 " --> pdb=" O MET I 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.775A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET I 34 " --> pdb=" O MET I 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1431 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: 5.57 Time building geometry restraints manager: 9.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5580 1.35 - 1.47: 4613 1.47 - 1.59: 7765 1.59 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 18126 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" N GLU I 1 " pdb=" CA GLU I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLU D 1 " pdb=" CA GLU D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 18121 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.82: 542 106.82 - 113.64: 10605 113.64 - 120.46: 6124 120.46 - 127.29: 7081 127.29 - 134.11: 218 Bond angle restraints: 24570 Sorted by residual: angle pdb=" N SER I 97 " pdb=" CA SER I 97 " pdb=" C SER I 97 " ideal model delta sigma weight residual 107.49 113.32 -5.83 1.74e+00 3.30e-01 1.12e+01 angle pdb=" CA LEU F 494 " pdb=" CB LEU F 494 " pdb=" CG LEU F 494 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.25e+00 angle pdb=" CA CYS F 54 " pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " ideal model delta sigma weight residual 114.40 120.55 -6.15 2.30e+00 1.89e-01 7.14e+00 angle pdb=" N LEU A 544 " pdb=" CA LEU A 544 " pdb=" C LEU A 544 " ideal model delta sigma weight residual 114.04 110.77 3.27 1.24e+00 6.50e-01 6.97e+00 angle pdb=" CA LEU G 494 " pdb=" CB LEU G 494 " pdb=" CG LEU G 494 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 ... (remaining 24565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 11128 22.04 - 44.07: 860 44.07 - 66.11: 130 66.11 - 88.15: 83 88.15 - 110.19: 48 Dihedral angle restraints: 12249 sinusoidal: 6270 harmonic: 5979 Sorted by residual: dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -26.75 -59.25 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.73 55.73 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.35 55.35 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 12246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2517 0.055 - 0.109: 367 0.109 - 0.164: 129 0.164 - 0.219: 5 0.219 - 0.273: 12 Chirality restraints: 3030 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3027 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 571 " -0.014 2.00e-02 2.50e+03 1.03e-02 2.67e+00 pdb=" CG TRP A 571 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 571 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 571 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 571 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 571 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 571 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 571 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 571 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 571 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 69 " -0.011 2.00e-02 2.50e+03 9.12e-03 2.08e+00 pdb=" CG TRP G 69 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 69 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP G 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 69 " -0.013 2.00e-02 2.50e+03 8.76e-03 1.92e+00 pdb=" CG TRP C 69 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 69 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP C 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 69 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 386 2.66 - 3.22: 16864 3.22 - 3.78: 24668 3.78 - 4.34: 33616 4.34 - 4.90: 55177 Nonbonded interactions: 130711 Sorted by model distance: nonbonded pdb=" O3 NAG Q 1 " pdb=" O5 NAG Q 2 " model vdw 2.103 2.440 nonbonded pdb=" O3 NAG Z 1 " pdb=" O5 NAG Z 2 " model vdw 2.112 2.440 nonbonded pdb=" O3 NAG i 1 " pdb=" O5 NAG i 2 " model vdw 2.112 2.440 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.135 2.440 nonbonded pdb=" OG SER F 460 " pdb=" OD1 ASN F 462 " model vdw 2.145 2.440 ... (remaining 130706 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' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'S' selection = chain 'T' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'W' selection = chain 'a' selection = chain 'f' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.660 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 49.460 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.320 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.004 0.039 18126 Z= 0.256 Angle : 0.661 9.426 24570 Z= 0.290 Chirality : 0.049 0.273 3030 Planarity : 0.002 0.024 3003 Dihedral : 17.479 110.186 8280 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % 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: -0.80 (0.19), residues: 2040 helix: 1.20 (0.32), residues: 342 sheet: -0.51 (0.25), residues: 459 loop : -1.05 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 PHE 0.009 0.001 PHE C 288 TYR 0.004 0.001 TYR C 486 ARG 0.005 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8910 (t0) cc_final: 0.8623 (t0) REVERT: B 647 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 195 ASN cc_start: 0.8149 (p0) cc_final: 0.7834 (p0) REVERT: A 543 ASN cc_start: 0.8850 (t0) cc_final: 0.8477 (t0) REVERT: A 584 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 647 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 648 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 654 GLU cc_start: 0.8654 (tp30) cc_final: 0.8408 (tp30) REVERT: D 44 GLU cc_start: 0.8400 (mp0) cc_final: 0.8176 (mp0) REVERT: E 543 ASN cc_start: 0.8689 (t0) cc_final: 0.8295 (t0) REVERT: E 584 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8282 (tm-30) REVERT: E 647 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7850 (tm-30) REVERT: E 648 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 434 MET cc_start: 0.8500 (ttm) cc_final: 0.8227 (ttm) REVERT: I 44 GLU cc_start: 0.8415 (mp0) cc_final: 0.8179 (mp0) REVERT: I 82 MET cc_start: 0.8466 (mmp) cc_final: 0.8014 (mmp) outliers start: 4 outliers final: 3 residues processed: 192 average time/residue: 0.2837 time to fit residues: 84.4034 Evaluate side-chains 138 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain I residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 85 HIS G 103 GLN C 85 HIS F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18126 Z= 0.351 Angle : 0.668 12.458 24570 Z= 0.328 Chirality : 0.047 0.189 3030 Planarity : 0.003 0.038 3003 Dihedral : 13.153 70.908 4401 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.83 % Allowed : 8.76 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2040 helix: 0.75 (0.29), residues: 363 sheet: -0.93 (0.25), residues: 399 loop : -1.24 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 571 HIS 0.005 0.001 HIS F 374 PHE 0.028 0.002 PHE D 17 TYR 0.011 0.001 TYR D 79 ARG 0.003 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.872 Fit side-chains REVERT: B 543 ASN cc_start: 0.8816 (t0) cc_final: 0.8428 (t0) REVERT: B 647 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 654 GLU cc_start: 0.9226 (tp30) cc_final: 0.8989 (tp30) REVERT: G 195 ASN cc_start: 0.7806 (p0) cc_final: 0.7570 (p0) REVERT: H 51 MET cc_start: 0.8333 (tpt) cc_final: 0.8091 (tpt) REVERT: A 530 MET cc_start: 0.8246 (ttp) cc_final: 0.8012 (ttt) REVERT: A 543 ASN cc_start: 0.8792 (t0) cc_final: 0.8348 (t0) REVERT: A 584 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 647 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 648 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8609 (mm-30) REVERT: A 654 GLU cc_start: 0.8878 (tp30) cc_final: 0.8637 (tp30) REVERT: D 100 TYR cc_start: 0.9051 (m-80) cc_final: 0.8765 (m-80) REVERT: E 543 ASN cc_start: 0.8655 (t0) cc_final: 0.8180 (t0) REVERT: E 647 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8151 (tm-30) REVERT: E 648 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8685 (mm-30) REVERT: F 434 MET cc_start: 0.8529 (ttm) cc_final: 0.8294 (ttm) REVERT: I 44 GLU cc_start: 0.8459 (mp0) cc_final: 0.8232 (mp0) REVERT: I 82 MET cc_start: 0.8701 (mmp) cc_final: 0.8051 (mmp) outliers start: 15 outliers final: 12 residues processed: 147 average time/residue: 0.2711 time to fit residues: 62.6518 Evaluate side-chains 141 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 173 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18126 Z= 0.230 Angle : 0.568 12.338 24570 Z= 0.278 Chirality : 0.045 0.175 3030 Planarity : 0.003 0.031 3003 Dihedral : 10.301 54.599 4398 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.21 % Allowed : 11.24 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2040 helix: 0.98 (0.29), residues: 360 sheet: -0.91 (0.24), residues: 432 loop : -1.22 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 PHE 0.022 0.002 PHE C 288 TYR 0.015 0.001 TYR H 100G ARG 0.002 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 2.047 Fit side-chains REVERT: B 543 ASN cc_start: 0.8795 (t0) cc_final: 0.8362 (t0) REVERT: B 584 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 647 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 654 GLU cc_start: 0.9210 (tp30) cc_final: 0.8971 (tp30) REVERT: G 195 ASN cc_start: 0.7912 (p0) cc_final: 0.7666 (p0) REVERT: A 543 ASN cc_start: 0.8758 (t0) cc_final: 0.8303 (t0) REVERT: A 584 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 647 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 648 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8515 (mm-30) REVERT: A 654 GLU cc_start: 0.8925 (tp30) cc_final: 0.8698 (tp30) REVERT: C 210 PHE cc_start: 0.9047 (m-10) cc_final: 0.8804 (m-10) REVERT: D 13 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 100 TYR cc_start: 0.9050 (m-80) cc_final: 0.8802 (m-80) REVERT: E 543 ASN cc_start: 0.8640 (t0) cc_final: 0.8134 (t0) REVERT: E 647 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8283 (tm-30) REVERT: F 161 MET cc_start: 0.8259 (mmm) cc_final: 0.7862 (mmm) REVERT: F 434 MET cc_start: 0.8469 (ttm) cc_final: 0.8193 (ttm) REVERT: I 82 MET cc_start: 0.8736 (mmp) cc_final: 0.8130 (mmp) outliers start: 22 outliers final: 14 residues processed: 153 average time/residue: 0.2611 time to fit residues: 63.6167 Evaluate side-chains 139 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18126 Z= 0.283 Angle : 0.584 12.208 24570 Z= 0.288 Chirality : 0.045 0.189 3030 Planarity : 0.003 0.036 3003 Dihedral : 8.572 54.275 4398 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.09 % Allowed : 13.50 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2040 helix: 1.06 (0.29), residues: 360 sheet: -0.70 (0.25), residues: 411 loop : -1.36 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 571 HIS 0.005 0.001 HIS F 374 PHE 0.029 0.002 PHE D 17 TYR 0.014 0.001 TYR H 100G ARG 0.002 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.768 Fit side-chains REVERT: B 543 ASN cc_start: 0.8784 (t0) cc_final: 0.8329 (t0) REVERT: B 584 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 647 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 654 GLU cc_start: 0.9202 (tp30) cc_final: 0.8976 (tp30) REVERT: H 51 MET cc_start: 0.8400 (tpt) cc_final: 0.8076 (tpt) REVERT: A 543 ASN cc_start: 0.8783 (t0) cc_final: 0.8316 (t0) REVERT: A 584 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 633 LYS cc_start: 0.9191 (mttp) cc_final: 0.8923 (mptt) REVERT: A 647 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 648 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 654 GLU cc_start: 0.8922 (tp30) cc_final: 0.8704 (tp30) REVERT: C 210 PHE cc_start: 0.9102 (m-10) cc_final: 0.8849 (m-10) REVERT: D 100 TYR cc_start: 0.9061 (m-80) cc_final: 0.8758 (m-80) REVERT: E 535 MET cc_start: 0.9163 (mmm) cc_final: 0.8957 (mpp) REVERT: E 543 ASN cc_start: 0.8680 (t0) cc_final: 0.8216 (t0) REVERT: E 584 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7521 (tm-30) REVERT: E 647 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8292 (tm-30) REVERT: F 161 MET cc_start: 0.8368 (mmm) cc_final: 0.7939 (mmm) REVERT: F 434 MET cc_start: 0.8489 (ttm) cc_final: 0.8282 (ttm) REVERT: I 82 MET cc_start: 0.8774 (mmp) cc_final: 0.8134 (mmp) outliers start: 38 outliers final: 25 residues processed: 167 average time/residue: 0.2742 time to fit residues: 72.3777 Evaluate side-chains 154 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18126 Z= 0.332 Angle : 0.610 13.353 24570 Z= 0.300 Chirality : 0.045 0.173 3030 Planarity : 0.003 0.036 3003 Dihedral : 7.985 54.414 4398 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.81 % Allowed : 14.49 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2040 helix: 1.06 (0.29), residues: 360 sheet: -0.46 (0.23), residues: 462 loop : -1.49 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 571 HIS 0.005 0.001 HIS F 374 PHE 0.023 0.002 PHE D 17 TYR 0.010 0.001 TYR H 100G ARG 0.002 0.000 ARG F 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 132 time to evaluate : 2.244 Fit side-chains REVERT: B 543 ASN cc_start: 0.8809 (t0) cc_final: 0.8348 (t0) REVERT: B 584 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 647 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 654 GLU cc_start: 0.9179 (tp30) cc_final: 0.8946 (tp30) REVERT: H 51 MET cc_start: 0.8410 (tpt) cc_final: 0.8087 (tpt) REVERT: A 543 ASN cc_start: 0.8786 (t0) cc_final: 0.8314 (t0) REVERT: A 544 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 584 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 647 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 648 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 654 GLU cc_start: 0.8926 (tp30) cc_final: 0.8718 (tp30) REVERT: D 82 MET cc_start: 0.8349 (tpp) cc_final: 0.7151 (mmm) REVERT: D 100 TYR cc_start: 0.9105 (m-80) cc_final: 0.8775 (m-80) REVERT: E 543 ASN cc_start: 0.8704 (t0) cc_final: 0.8233 (t0) REVERT: E 584 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 647 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8273 (tm-30) REVERT: F 475 MET cc_start: 0.8686 (tpp) cc_final: 0.8462 (tpp) REVERT: I 82 MET cc_start: 0.8832 (mmp) cc_final: 0.8176 (mmp) REVERT: I 82 LEU cc_start: 0.9002 (mm) cc_final: 0.8788 (mm) outliers start: 51 outliers final: 38 residues processed: 179 average time/residue: 0.2716 time to fit residues: 77.3381 Evaluate side-chains 167 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.0040 chunk 180 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18126 Z= 0.137 Angle : 0.542 13.181 24570 Z= 0.264 Chirality : 0.043 0.159 3030 Planarity : 0.003 0.035 3003 Dihedral : 7.025 55.207 4398 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.93 % Allowed : 16.47 % Favored : 81.60 % 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: -0.95 (0.19), residues: 2040 helix: 1.32 (0.29), residues: 360 sheet: -0.53 (0.23), residues: 486 loop : -1.33 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 PHE 0.023 0.001 PHE C 288 TYR 0.012 0.001 TYR H 100G ARG 0.002 0.000 ARG F 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 2.106 Fit side-chains REVERT: B 543 ASN cc_start: 0.8757 (t0) cc_final: 0.8291 (t0) REVERT: B 584 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 647 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 654 GLU cc_start: 0.9149 (tp30) cc_final: 0.8893 (tp30) REVERT: G 195 ASN cc_start: 0.8003 (p0) cc_final: 0.7770 (p0) REVERT: A 543 ASN cc_start: 0.8730 (t0) cc_final: 0.8240 (t0) REVERT: A 544 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 584 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 647 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 648 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8470 (mm-30) REVERT: D 30 ASN cc_start: 0.8962 (p0) cc_final: 0.8630 (p0) REVERT: E 543 ASN cc_start: 0.8645 (t0) cc_final: 0.8177 (t0) REVERT: I 82 MET cc_start: 0.8777 (mmp) cc_final: 0.8192 (mmp) REVERT: I 82 LEU cc_start: 0.8917 (mm) cc_final: 0.8697 (mm) outliers start: 35 outliers final: 23 residues processed: 179 average time/residue: 0.2702 time to fit residues: 76.6065 Evaluate side-chains 153 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 124 optimal weight: 0.0980 chunk 121 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100CASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18126 Z= 0.182 Angle : 0.552 12.795 24570 Z= 0.268 Chirality : 0.043 0.154 3030 Planarity : 0.003 0.035 3003 Dihedral : 6.700 55.428 4398 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.26 % Allowed : 16.58 % Favored : 81.16 % 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: -0.89 (0.19), residues: 2040 helix: 1.35 (0.29), residues: 360 sheet: -0.43 (0.23), residues: 486 loop : -1.31 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 PHE 0.026 0.001 PHE H 17 TYR 0.018 0.001 TYR D 100G ARG 0.001 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.933 Fit side-chains REVERT: B 543 ASN cc_start: 0.8816 (t0) cc_final: 0.8385 (t0) REVERT: B 584 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 647 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 543 ASN cc_start: 0.8754 (t0) cc_final: 0.8310 (t0) REVERT: A 574 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8248 (ptpt) REVERT: A 584 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 647 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 648 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8455 (mm-30) REVERT: C 475 MET cc_start: 0.8742 (tpp) cc_final: 0.8511 (tpp) REVERT: D 30 ASN cc_start: 0.8949 (p0) cc_final: 0.8609 (p0) REVERT: D 105 ARG cc_start: 0.8490 (mmp80) cc_final: 0.8244 (mmm160) REVERT: E 535 MET cc_start: 0.8991 (tpp) cc_final: 0.8162 (mpp) REVERT: E 543 ASN cc_start: 0.8681 (t0) cc_final: 0.8200 (t0) REVERT: E 647 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 161 MET cc_start: 0.8132 (mmm) cc_final: 0.7760 (mmm) REVERT: F 288 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8160 (p90) REVERT: F 426 MET cc_start: 0.8620 (ptm) cc_final: 0.8412 (ptm) REVERT: F 475 MET cc_start: 0.8668 (tpp) cc_final: 0.8444 (tpp) REVERT: I 82 MET cc_start: 0.8749 (mmp) cc_final: 0.7906 (mmp) outliers start: 41 outliers final: 29 residues processed: 169 average time/residue: 0.2728 time to fit residues: 74.0055 Evaluate side-chains 159 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 100 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18126 Z= 0.208 Angle : 0.563 14.018 24570 Z= 0.273 Chirality : 0.043 0.157 3030 Planarity : 0.003 0.033 3003 Dihedral : 6.541 55.443 4398 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.31 % Allowed : 16.75 % Favored : 80.94 % 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: -0.90 (0.19), residues: 2040 helix: 1.34 (0.29), residues: 360 sheet: -0.34 (0.23), residues: 504 loop : -1.37 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 PHE 0.025 0.001 PHE H 17 TYR 0.015 0.001 TYR D 100G ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8829 (t0) cc_final: 0.8397 (t0) REVERT: B 584 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 647 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 543 ASN cc_start: 0.8751 (t0) cc_final: 0.8300 (t0) REVERT: A 574 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8261 (ptpt) REVERT: A 584 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 647 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 648 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8442 (mm-30) REVERT: D 105 ARG cc_start: 0.8516 (mmp80) cc_final: 0.8279 (mmm160) REVERT: E 535 MET cc_start: 0.9023 (tpp) cc_final: 0.8164 (mpp) REVERT: E 543 ASN cc_start: 0.8645 (t0) cc_final: 0.8189 (t0) REVERT: E 584 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7893 (tm-30) REVERT: F 161 MET cc_start: 0.8133 (mmm) cc_final: 0.7756 (mmm) REVERT: F 288 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8162 (p90) REVERT: F 475 MET cc_start: 0.8745 (tpp) cc_final: 0.8088 (tpp) REVERT: I 82 MET cc_start: 0.8753 (mmp) cc_final: 0.7892 (mmp) REVERT: I 82 LEU cc_start: 0.8970 (mm) cc_final: 0.8573 (mm) outliers start: 42 outliers final: 34 residues processed: 171 average time/residue: 0.2716 time to fit residues: 73.9901 Evaluate side-chains 164 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18126 Z= 0.317 Angle : 0.621 14.258 24570 Z= 0.303 Chirality : 0.044 0.176 3030 Planarity : 0.003 0.034 3003 Dihedral : 6.676 55.351 4398 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.59 % Allowed : 16.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2040 helix: 1.22 (0.29), residues: 360 sheet: -0.46 (0.23), residues: 501 loop : -1.45 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 479 HIS 0.004 0.001 HIS C 374 PHE 0.024 0.002 PHE D 17 TYR 0.010 0.001 TYR D 100G ARG 0.003 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 2.711 Fit side-chains REVERT: B 543 ASN cc_start: 0.8846 (t0) cc_final: 0.8401 (t0) REVERT: B 584 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 647 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 543 ASN cc_start: 0.8767 (t0) cc_final: 0.8276 (t0) REVERT: A 574 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8287 (ptpt) REVERT: A 584 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 647 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 648 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8494 (mm-30) REVERT: C 265 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 271 MET cc_start: 0.7759 (mmm) cc_final: 0.7513 (mmm) REVERT: D 105 ARG cc_start: 0.8538 (mmp80) cc_final: 0.8309 (mmm160) REVERT: E 535 MET cc_start: 0.9034 (tpp) cc_final: 0.8134 (mpp) REVERT: E 543 ASN cc_start: 0.8685 (t0) cc_final: 0.8218 (t0) REVERT: F 161 MET cc_start: 0.8168 (mmm) cc_final: 0.7772 (mmm) REVERT: F 288 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8406 (p90) REVERT: F 475 MET cc_start: 0.8828 (tpp) cc_final: 0.8224 (tpp) REVERT: I 82 MET cc_start: 0.8848 (mmp) cc_final: 0.8036 (mmp) REVERT: I 82 LEU cc_start: 0.8985 (mm) cc_final: 0.8568 (mm) outliers start: 47 outliers final: 41 residues processed: 173 average time/residue: 0.2652 time to fit residues: 73.5305 Evaluate side-chains 171 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 6.9990 chunk 119 optimal weight: 0.0470 chunk 93 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 0.0370 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 203 GLN I 100CASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18126 Z= 0.152 Angle : 0.556 14.421 24570 Z= 0.270 Chirality : 0.042 0.159 3030 Planarity : 0.003 0.046 3003 Dihedral : 6.305 55.441 4398 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.76 % Allowed : 17.96 % Favored : 80.28 % 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: -0.79 (0.18), residues: 2040 helix: 1.38 (0.29), residues: 360 sheet: -0.19 (0.23), residues: 468 loop : -1.30 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 PHE 0.024 0.001 PHE H 17 TYR 0.007 0.001 TYR D 100G ARG 0.002 0.000 ARG A 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8826 (t0) cc_final: 0.8375 (t0) REVERT: B 584 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 647 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8244 (tm-30) REVERT: G 195 ASN cc_start: 0.8100 (p0) cc_final: 0.7878 (p0) REVERT: H 51 MET cc_start: 0.8507 (tpt) cc_final: 0.8034 (tpp) REVERT: A 543 ASN cc_start: 0.8699 (t0) cc_final: 0.8242 (t0) REVERT: A 584 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 647 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 648 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 265 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8511 (mt) REVERT: C 271 MET cc_start: 0.7707 (mmm) cc_final: 0.7465 (mmm) REVERT: D 30 ASN cc_start: 0.8950 (p0) cc_final: 0.8609 (p0) REVERT: D 105 ARG cc_start: 0.8554 (mmp80) cc_final: 0.8325 (mmm160) REVERT: E 535 MET cc_start: 0.9043 (tpp) cc_final: 0.8212 (mpp) REVERT: E 543 ASN cc_start: 0.8650 (t0) cc_final: 0.8188 (t0) REVERT: F 161 MET cc_start: 0.8063 (mmm) cc_final: 0.7675 (mmm) REVERT: F 475 MET cc_start: 0.8736 (tpp) cc_final: 0.8123 (tpp) REVERT: I 82 MET cc_start: 0.8753 (mmp) cc_final: 0.8207 (mmp) REVERT: I 82 LEU cc_start: 0.8973 (mm) cc_final: 0.8760 (mm) outliers start: 32 outliers final: 29 residues processed: 167 average time/residue: 0.2701 time to fit residues: 71.1069 Evaluate side-chains 159 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 151 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060438 restraints weight = 48809.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063479 restraints weight = 29925.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064997 restraints weight = 19287.968| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18126 Z= 0.253 Angle : 0.587 13.994 24570 Z= 0.285 Chirality : 0.043 0.163 3030 Planarity : 0.003 0.041 3003 Dihedral : 6.316 55.449 4398 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.15 % Allowed : 17.58 % Favored : 80.28 % 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: -0.89 (0.18), residues: 2040 helix: 1.36 (0.29), residues: 360 sheet: -0.35 (0.23), residues: 504 loop : -1.36 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 479 HIS 0.004 0.001 HIS C 374 PHE 0.024 0.002 PHE H 17 TYR 0.007 0.001 TYR D 100G ARG 0.003 0.000 ARG H 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.10 seconds wall clock time: 52 minutes 18.20 seconds (3138.20 seconds total)