Starting phenix.real_space_refine on Tue Aug 6 20:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/08_2024/8tng_41415.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/08_2024/8tng_41415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/08_2024/8tng_41415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/08_2024/8tng_41415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/08_2024/8tng_41415.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/08_2024/8tng_41415.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 10905 2.51 5 N 2966 2.21 5 O 3501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 321": "OD1" <-> "OD2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 457": "OD1" <-> "OD2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17495 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 910 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" 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: 9.82, per 1000 atoms: 0.56 Number of scatterers: 17495 At special positions: 0 Unit cell: (135.42, 134.31, 125.43, 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 3501 8.00 N 2966 7.00 C 10905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 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=2.04 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=2.04 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 C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 99 " 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 S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 197 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 197 " " NAG C 607 " - " ASN C 301 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 197 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 363 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 295 " " NAG c 1 " - " ASN E 332 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 386 " Time building additional restraints: 8.59 Conformation dependent library (CDL) restraints added in 3.3 seconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 39 sheets defined 16.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.248A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 removed outlier: 4.226A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.538A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.469A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.687A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.951A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.663A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.199A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.101A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 350 removed outlier: 4.110A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.965A pdb=" N GLY C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.738A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.514A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.953A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.557A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.894A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.924A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.551A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 94 through 98' Processing helix chain 'E' and resid 99 through 117 removed outlier: 4.141A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.512A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 removed outlier: 4.320A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.578A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.066A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.518A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 removed outlier: 4.194A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.490A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.097A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.672A pdb=" N ARG A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 413 through 417 removed outlier: 3.941A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 308 removed outlier: 4.229A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 removed outlier: 4.436A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 361 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.473A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.805A pdb=" N ILE A 424 " --> pdb=" O MET A 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.109A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.653A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 176 removed outlier: 3.832A pdb=" N CYS C 131 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.580A pdb=" N ARG C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 413 through 417 removed outlier: 4.121A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain 'C' and resid 393 through 395 removed outlier: 4.228A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 382 through 383 removed outlier: 4.525A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 495 through 499 removed outlier: 4.635A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.095A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 172 through 176 removed outlier: 3.684A pdb=" N CYS E 131 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=AC9, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.096A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'E' and resid 393 through 395 removed outlier: 4.143A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 361 " --> pdb=" O SER E 393 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 377 through 378 removed outlier: 4.419A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.882A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.522A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 45 through 50 removed outlier: 3.786A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N CYS H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE H 34 " --> pdb=" O CYS H 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.857A pdb=" N MET I 82 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.049A pdb=" N GLY I 10 " --> pdb=" O GLN I 108 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 47 through 50 removed outlier: 4.857A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.824A pdb=" N MET J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.704A pdb=" N THR J 110 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR J 90 " --> pdb=" O THR J 107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 45 through 50 removed outlier: 3.697A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL J 48 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE J 34 " --> pdb=" O CYS J 50 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1101 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: 4.96 Time building geometry restraints manager: 9.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3116 1.33 - 1.46: 6566 1.46 - 1.60: 7981 1.60 - 1.73: 0 1.73 - 1.86: 162 Bond restraints: 17825 Sorted by residual: bond pdb=" C1 NAG E 605 " pdb=" O5 NAG E 605 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA ALA A 319 " pdb=" CB ALA A 319 " ideal model delta sigma weight residual 1.533 1.472 0.061 1.60e-02 3.91e+03 1.45e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.528 1.472 0.056 1.48e-02 4.57e+03 1.41e+01 bond pdb=" C TYR A 318 " pdb=" O TYR A 318 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 17820 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.20: 369 106.20 - 113.17: 10145 113.17 - 120.14: 5799 120.14 - 127.11: 7652 127.11 - 134.08: 216 Bond angle restraints: 24181 Sorted by residual: angle pdb=" CA PHE E 317 " pdb=" C PHE E 317 " pdb=" O PHE E 317 " ideal model delta sigma weight residual 120.32 112.50 7.82 1.11e+00 8.12e-01 4.97e+01 angle pdb=" CA PHE E 317 " pdb=" CB PHE E 317 " pdb=" CG PHE E 317 " ideal model delta sigma weight residual 113.80 120.81 -7.01 1.00e+00 1.00e+00 4.92e+01 angle pdb=" CA CYS E 501 " pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " ideal model delta sigma weight residual 114.40 125.47 -11.07 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CA PHE E 317 " pdb=" C PHE E 317 " pdb=" N TYR E 318 " ideal model delta sigma weight residual 116.32 122.74 -6.42 1.38e+00 5.25e-01 2.17e+01 angle pdb=" N GLU I 30 " pdb=" CA GLU I 30 " pdb=" C GLU I 30 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 ... (remaining 24176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.12: 10530 25.12 - 50.25: 965 50.25 - 75.37: 159 75.37 - 100.50: 33 100.50 - 125.62: 10 Dihedral angle restraints: 11697 sinusoidal: 5675 harmonic: 6022 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -0.15 -85.85 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 11.03 81.97 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 12.78 80.22 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 11694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 2893 0.165 - 0.329: 22 0.329 - 0.494: 3 0.494 - 0.658: 3 0.658 - 0.823: 1 Chirality restraints: 2922 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.50e+00 ... (remaining 2919 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 301 " 0.001 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN E 301 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN E 301 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN E 301 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " -0.037 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" CG ASN A 295 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " -0.039 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN B 637 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.040 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 386 2.65 - 3.22: 15651 3.22 - 3.78: 23641 3.78 - 4.34: 30968 4.34 - 4.90: 52616 Nonbonded interactions: 123262 Sorted by model distance: nonbonded pdb=" OG SER H 52 " pdb=" OG SER H 57 " model vdw 2.093 3.040 nonbonded pdb=" OD1 ASN H 96 " pdb=" N ARG H 97 " model vdw 2.126 3.120 nonbonded pdb=" OG SER H 33 " pdb=" O LEU H 51 " model vdw 2.154 3.040 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASN J 96 " pdb=" N ARG J 97 " model vdw 2.167 3.120 ... (remaining 123257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 505 or resid 601 through 607)) selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 through 607)) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'H' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 113)) selection = (chain 'I' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 113)) selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 48.440 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17825 Z= 0.308 Angle : 0.816 11.573 24181 Z= 0.426 Chirality : 0.057 0.823 2922 Planarity : 0.004 0.063 3009 Dihedral : 18.195 125.624 7689 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.75 % Favored : 88.81 % Rotamer: Outliers : 0.60 % Allowed : 33.66 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.18), residues: 2065 helix: -0.78 (0.30), residues: 347 sheet: -0.25 (0.27), residues: 404 loop : -2.44 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 35 HIS 0.004 0.001 HIS C 374 PHE 0.034 0.002 PHE C 233 TYR 0.023 0.001 TYR C 486 ARG 0.006 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 301 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 HIS cc_start: 0.7730 (m-70) cc_final: 0.7341 (m90) REVERT: E 475 MET cc_start: 0.7575 (tpp) cc_final: 0.7298 (tpp) REVERT: F 639 THR cc_start: 0.7307 (m) cc_final: 0.6930 (p) outliers start: 11 outliers final: 6 residues processed: 310 average time/residue: 0.3362 time to fit residues: 150.0258 Evaluate side-chains 168 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain H residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 188 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN E 66 HIS ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17825 Z= 0.269 Angle : 0.771 9.001 24181 Z= 0.396 Chirality : 0.047 0.375 2922 Planarity : 0.004 0.063 3009 Dihedral : 11.300 116.068 3832 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.04 % Favored : 88.47 % Rotamer: Outliers : 5.92 % Allowed : 28.78 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 2065 helix: -0.65 (0.29), residues: 348 sheet: -0.37 (0.25), residues: 486 loop : -2.61 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 69 HIS 0.005 0.001 HIS H 61 PHE 0.018 0.001 PHE E 382 TYR 0.012 0.001 TYR E 318 ARG 0.008 0.001 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 189 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.8358 (p-80) cc_final: 0.7988 (p-80) REVERT: A 370 GLU cc_start: 0.7125 (mp0) cc_final: 0.6182 (mp0) REVERT: H 3 GLN cc_start: 0.7641 (pm20) cc_final: 0.7304 (pm20) REVERT: I 3 GLN cc_start: 0.7806 (pm20) cc_final: 0.7527 (pm20) REVERT: J 3 GLN cc_start: 0.8070 (pm20) cc_final: 0.7751 (pm20) REVERT: J 96 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8047 (t0) outliers start: 108 outliers final: 38 residues processed: 284 average time/residue: 0.2850 time to fit residues: 122.3276 Evaluate side-chains 197 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 188 optimal weight: 0.0670 chunk 203 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17825 Z= 0.264 Angle : 0.735 9.083 24181 Z= 0.375 Chirality : 0.046 0.283 2922 Planarity : 0.004 0.061 3009 Dihedral : 10.109 111.467 3830 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.31 % Favored : 89.15 % Rotamer: Outliers : 4.22 % Allowed : 29.61 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 2065 helix: -0.79 (0.28), residues: 363 sheet: -0.41 (0.24), residues: 489 loop : -2.57 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 479 HIS 0.007 0.001 HIS C 374 PHE 0.034 0.002 PHE B 519 TYR 0.011 0.001 TYR D 638 ARG 0.004 0.000 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 172 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 ASN cc_start: 0.7361 (t0) cc_final: 0.7111 (t0) REVERT: D 626 MET cc_start: 0.6896 (tpp) cc_final: 0.4831 (tpp) REVERT: H 2 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7182 (t) REVERT: H 3 GLN cc_start: 0.7615 (pm20) cc_final: 0.7242 (pm20) REVERT: J 3 GLN cc_start: 0.8000 (pm20) cc_final: 0.7657 (pm20) REVERT: J 96 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8130 (t0) outliers start: 77 outliers final: 39 residues processed: 239 average time/residue: 0.2734 time to fit residues: 100.1585 Evaluate side-chains 188 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 246 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17825 Z= 0.444 Angle : 0.819 11.778 24181 Z= 0.413 Chirality : 0.047 0.293 2922 Planarity : 0.004 0.064 3009 Dihedral : 9.507 111.189 3830 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.72 % Favored : 87.85 % Rotamer: Outliers : 5.26 % Allowed : 28.29 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 2065 helix: -0.62 (0.28), residues: 341 sheet: -0.58 (0.24), residues: 450 loop : -2.47 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 96 HIS 0.005 0.001 HIS C 374 PHE 0.022 0.002 PHE J 27 TYR 0.015 0.001 TYR B 586 ARG 0.005 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 147 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7936 (mpp) cc_final: 0.7432 (mpp) REVERT: A 475 MET cc_start: 0.7205 (tpt) cc_final: 0.6666 (tpp) REVERT: C 478 ASN cc_start: 0.7237 (p0) cc_final: 0.6960 (p0) REVERT: H 3 GLN cc_start: 0.7699 (pm20) cc_final: 0.7407 (pm20) REVERT: H 4 LEU cc_start: 0.7718 (mt) cc_final: 0.7422 (tp) REVERT: J 96 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8225 (t0) outliers start: 96 outliers final: 57 residues processed: 234 average time/residue: 0.2832 time to fit residues: 101.6911 Evaluate side-chains 189 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17825 Z= 0.244 Angle : 0.728 9.052 24181 Z= 0.368 Chirality : 0.046 0.283 2922 Planarity : 0.004 0.062 3009 Dihedral : 8.880 109.904 3830 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.36 % Favored : 89.20 % Rotamer: Outliers : 3.89 % Allowed : 29.00 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.18), residues: 2065 helix: -0.60 (0.28), residues: 352 sheet: -0.54 (0.23), residues: 502 loop : -2.45 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 479 HIS 0.004 0.001 HIS C 374 PHE 0.015 0.001 PHE J 37 TYR 0.025 0.001 TYR A 61 ARG 0.010 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 153 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7801 (mpp) cc_final: 0.7336 (mpp) REVERT: E 104 MET cc_start: 0.8598 (ppp) cc_final: 0.8393 (ppp) REVERT: E 387 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8195 (p) REVERT: H 2 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7153 (t) REVERT: H 3 GLN cc_start: 0.7648 (pm20) cc_final: 0.7389 (pm20) REVERT: H 82 MET cc_start: 0.7982 (mmm) cc_final: 0.7699 (mmm) REVERT: I 3 GLN cc_start: 0.7908 (pm20) cc_final: 0.7695 (pm20) REVERT: J 3 GLN cc_start: 0.7799 (pm20) cc_final: 0.7467 (pm20) outliers start: 71 outliers final: 46 residues processed: 218 average time/residue: 0.2857 time to fit residues: 95.6930 Evaluate side-chains 185 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN E 188 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17825 Z= 0.205 Angle : 0.726 9.674 24181 Z= 0.364 Chirality : 0.046 0.267 2922 Planarity : 0.004 0.060 3009 Dihedral : 8.452 108.506 3829 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.36 % Favored : 89.20 % Rotamer: Outliers : 3.34 % Allowed : 28.67 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 2065 helix: -0.36 (0.29), residues: 352 sheet: -0.47 (0.24), residues: 483 loop : -2.37 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 PHE 0.026 0.001 PHE J 27 TYR 0.011 0.001 TYR E 318 ARG 0.012 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 150 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8112 (t) REVERT: E 104 MET cc_start: 0.8589 (ppp) cc_final: 0.8355 (ppp) REVERT: E 150 MET cc_start: 0.8207 (mpp) cc_final: 0.7533 (mpp) REVERT: E 387 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (p) REVERT: H 2 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7056 (t) REVERT: I 3 GLN cc_start: 0.7915 (pm20) cc_final: 0.7696 (pm20) REVERT: J 3 GLN cc_start: 0.7716 (pm20) cc_final: 0.7434 (pm20) outliers start: 61 outliers final: 47 residues processed: 205 average time/residue: 0.2845 time to fit residues: 91.2145 Evaluate side-chains 186 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 136 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN D 590 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17825 Z= 0.376 Angle : 0.790 11.748 24181 Z= 0.394 Chirality : 0.046 0.292 2922 Planarity : 0.004 0.060 3009 Dihedral : 8.442 108.404 3828 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.38 % Favored : 88.18 % Rotamer: Outliers : 4.28 % Allowed : 28.34 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.18), residues: 2065 helix: -0.11 (0.30), residues: 325 sheet: -0.34 (0.26), residues: 392 loop : -2.40 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 479 HIS 0.004 0.001 HIS H 61 PHE 0.027 0.002 PHE B 522 TYR 0.019 0.001 TYR C 61 ARG 0.012 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 137 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8333 (p) REVERT: E 150 MET cc_start: 0.8388 (mpp) cc_final: 0.7780 (mpp) REVERT: H 2 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7278 (t) REVERT: I 3 GLN cc_start: 0.8089 (pm20) cc_final: 0.7856 (pm20) REVERT: J 3 GLN cc_start: 0.7733 (pm20) cc_final: 0.7376 (pm20) REVERT: J 57 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8241 (p) outliers start: 78 outliers final: 50 residues processed: 206 average time/residue: 0.2706 time to fit residues: 86.9282 Evaluate side-chains 183 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17825 Z= 0.199 Angle : 0.753 10.577 24181 Z= 0.373 Chirality : 0.046 0.266 2922 Planarity : 0.004 0.056 3009 Dihedral : 8.046 107.058 3827 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.39 % Favored : 90.22 % Rotamer: Outliers : 2.63 % Allowed : 29.61 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 2065 helix: -0.08 (0.30), residues: 338 sheet: -0.36 (0.25), residues: 464 loop : -2.39 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 PHE 0.028 0.001 PHE J 27 TYR 0.025 0.001 TYR C 61 ARG 0.013 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 150 MET cc_start: 0.8271 (mpp) cc_final: 0.7709 (mpp) REVERT: I 3 GLN cc_start: 0.7789 (pm20) cc_final: 0.7582 (pm20) REVERT: J 3 GLN cc_start: 0.7495 (pm20) cc_final: 0.7286 (pm20) outliers start: 48 outliers final: 37 residues processed: 202 average time/residue: 0.2807 time to fit residues: 87.9899 Evaluate side-chains 180 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 30.0000 chunk 174 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 0.0030 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN E 478 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17825 Z= 0.208 Angle : 0.751 11.699 24181 Z= 0.371 Chirality : 0.046 0.251 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.855 105.716 3827 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.22 % Favored : 89.39 % Rotamer: Outliers : 2.19 % Allowed : 30.32 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.18), residues: 2065 helix: -0.15 (0.30), residues: 342 sheet: -0.42 (0.24), residues: 478 loop : -2.35 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 479 HIS 0.004 0.001 HIS C 216 PHE 0.019 0.001 PHE B 519 TYR 0.021 0.001 TYR C 61 ARG 0.015 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 150 MET cc_start: 0.8228 (mpp) cc_final: 0.7694 (mpp) REVERT: E 387 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8224 (p) REVERT: J 3 GLN cc_start: 0.7738 (pm20) cc_final: 0.7449 (pm20) outliers start: 40 outliers final: 36 residues processed: 183 average time/residue: 0.2802 time to fit residues: 79.3878 Evaluate side-chains 181 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 30.0000 chunk 119 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17825 Z= 0.385 Angle : 0.835 11.916 24181 Z= 0.412 Chirality : 0.046 0.302 2922 Planarity : 0.005 0.068 3009 Dihedral : 8.151 105.958 3827 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.33 % Favored : 88.28 % Rotamer: Outliers : 2.30 % Allowed : 30.37 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.18), residues: 2065 helix: -0.17 (0.29), residues: 333 sheet: -0.47 (0.25), residues: 418 loop : -2.37 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 479 HIS 0.005 0.001 HIS E 105 PHE 0.027 0.002 PHE J 27 TYR 0.017 0.001 TYR C 61 ARG 0.017 0.001 ARG D 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 150 MET cc_start: 0.8356 (mpp) cc_final: 0.7772 (mpp) outliers start: 42 outliers final: 39 residues processed: 173 average time/residue: 0.3009 time to fit residues: 79.7207 Evaluate side-chains 175 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.032085 restraints weight = 99642.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033408 restraints weight = 55508.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.034382 restraints weight = 38066.769| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17825 Z= 0.209 Angle : 0.787 11.821 24181 Z= 0.387 Chirality : 0.046 0.269 2922 Planarity : 0.004 0.055 3009 Dihedral : 7.819 104.513 3827 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.44 % Favored : 90.17 % Rotamer: Outliers : 2.30 % Allowed : 30.59 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 2065 helix: -0.25 (0.29), residues: 354 sheet: -0.53 (0.24), residues: 478 loop : -2.28 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 479 HIS 0.003 0.001 HIS C 374 PHE 0.015 0.001 PHE B 519 TYR 0.019 0.001 TYR C 61 ARG 0.015 0.001 ARG B 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.96 seconds wall clock time: 56 minutes 39.90 seconds (3399.90 seconds total)