Starting phenix.real_space_refine on Mon Jul 22 07:53:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/07_2024/8tng_41415.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/07_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_41415/07_2024/8tng_41415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/07_2024/8tng_41415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/07_2024/8tng_41415.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tng_41415/07_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.81, 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: 7.64 Conformation dependent library (CDL) restraints added in 3.2 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: 1.86 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: 4.92 Time building geometry restraints manager: 8.33 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 2.440 nonbonded pdb=" OD1 ASN H 96 " pdb=" N ARG H 97 " model vdw 2.126 2.520 nonbonded pdb=" OG SER H 33 " pdb=" O LEU H 51 " model vdw 2.154 2.440 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.166 2.440 nonbonded pdb=" OD1 ASN J 96 " pdb=" N ARG J 97 " model vdw 2.167 2.520 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 1.860 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 45.560 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.140 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.360 ------------------------------------------------------------------------------- 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 : 2.139 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: 0.3306 time to fit residues: 148.3173 Evaluate side-chains 168 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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: 3.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.0570 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** 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: 0.7834 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17825 Z= 0.303 Angle : 0.762 8.932 24181 Z= 0.389 Chirality : 0.047 0.333 2922 Planarity : 0.004 0.065 3009 Dihedral : 11.412 114.690 3832 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.67 % Favored : 87.85 % Rotamer: Outliers : 6.69 % Allowed : 30.65 % Favored : 62.66 % 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: -2.56 (0.18), residues: 2065 helix: -0.93 (0.28), residues: 374 sheet: -0.39 (0.25), residues: 450 loop : -2.60 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 69 HIS 0.005 0.001 HIS H 61 PHE 0.020 0.002 PHE E 382 TYR 0.013 0.002 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 302 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 180 time to evaluate : 1.824 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: A 72 HIS cc_start: 0.8375 (p-80) cc_final: 0.8013 (p-80) REVERT: A 326 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8948 (mm) REVERT: C 280 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7704 (m-40) REVERT: H 3 GLN cc_start: 0.7528 (pm20) cc_final: 0.7067 (pm20) REVERT: I 3 GLN cc_start: 0.7998 (pm20) cc_final: 0.7680 (pm20) outliers start: 122 outliers final: 43 residues processed: 289 average time/residue: 0.2802 time to fit residues: 122.6247 Evaluate side-chains 193 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 LYS 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 A residue 326 ILE Chi-restraints excluded: chain A residue 337 THR 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 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 89 VAL 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 337 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL 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: 10.0000 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 203 optimal weight: 0.0570 chunk 167 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 overall best weight: 2.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** 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: 0.7863 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17825 Z= 0.239 Angle : 0.718 9.441 24181 Z= 0.363 Chirality : 0.046 0.275 2922 Planarity : 0.004 0.062 3009 Dihedral : 10.286 110.308 3830 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.65 % Favored : 88.81 % Rotamer: Outliers : 4.39 % Allowed : 31.52 % Favored : 64.09 % 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: -2.49 (0.18), residues: 2065 helix: -0.78 (0.28), residues: 366 sheet: -0.40 (0.24), residues: 489 loop : -2.61 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 69 HIS 0.006 0.001 HIS C 374 PHE 0.036 0.002 PHE B 519 TYR 0.014 0.001 TYR D 638 ARG 0.007 0.000 ARG C 500 *********************** 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 246 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 166 time to evaluate : 1.949 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: D 626 MET cc_start: 0.6771 (tpp) cc_final: 0.5044 (tpp) REVERT: E 150 MET cc_start: 0.8206 (mpp) cc_final: 0.7694 (mpp) REVERT: H 2 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7191 (t) REVERT: H 3 GLN cc_start: 0.7375 (pm20) cc_final: 0.6991 (pm20) REVERT: I 3 GLN cc_start: 0.7729 (pm20) cc_final: 0.7349 (pm20) REVERT: J 3 GLN cc_start: 0.8168 (pm20) cc_final: 0.7795 (pm20) outliers start: 80 outliers final: 42 residues processed: 238 average time/residue: 0.2779 time to fit residues: 101.0733 Evaluate side-chains 190 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 LYS 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 C residue 100 MET 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 326 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 202 THR 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 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 639 THR 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 72 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 THR 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: 7.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 0.0970 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 188 ASN ** 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: 0.7872 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17825 Z= 0.214 Angle : 0.704 11.275 24181 Z= 0.350 Chirality : 0.046 0.263 2922 Planarity : 0.004 0.060 3009 Dihedral : 9.489 107.818 3830 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.46 % Favored : 89.01 % Rotamer: Outliers : 4.39 % Allowed : 30.92 % Favored : 64.69 % 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: -2.41 (0.18), residues: 2065 helix: -0.77 (0.28), residues: 372 sheet: -0.22 (0.25), residues: 481 loop : -2.61 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 571 HIS 0.004 0.001 HIS C 374 PHE 0.026 0.001 PHE J 27 TYR 0.018 0.001 TYR B 586 ARG 0.005 0.000 ARG C 500 *********************** 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: 80 poor density : 163 time to evaluate : 2.075 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: A 150 MET cc_start: 0.7776 (mtm) cc_final: 0.7539 (mpp) REVERT: A 475 MET cc_start: 0.7314 (tpp) cc_final: 0.7108 (tpp) REVERT: C 280 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (m110) REVERT: C 377 ASN cc_start: 0.7308 (t0) cc_final: 0.7108 (t0) REVERT: E 150 MET cc_start: 0.8004 (mpp) cc_final: 0.7769 (mpp) REVERT: E 280 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8245 (m110) REVERT: H 3 GLN cc_start: 0.7564 (pm20) cc_final: 0.7127 (pm20) REVERT: H 82 MET cc_start: 0.7950 (mmm) cc_final: 0.7680 (mmm) REVERT: I 3 GLN cc_start: 0.7536 (pm20) cc_final: 0.7168 (pm20) REVERT: J 3 GLN cc_start: 0.8105 (pm20) cc_final: 0.7685 (pm20) outliers start: 80 outliers final: 46 residues processed: 235 average time/residue: 0.3020 time to fit residues: 110.1517 Evaluate side-chains 198 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR 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 B residue 621 GLU Chi-restraints excluded: chain C residue 100 MET 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 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 536 THR 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 127 VAL Chi-restraints excluded: chain E residue 202 THR 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 280 ASN 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 H residue 18 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.0770 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** 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: 0.7872 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17825 Z= 0.188 Angle : 0.690 10.705 24181 Z= 0.342 Chirality : 0.045 0.257 2922 Planarity : 0.004 0.057 3009 Dihedral : 8.798 106.083 3830 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.27 % Favored : 89.30 % Rotamer: Outliers : 4.50 % Allowed : 30.59 % Favored : 64.91 % 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: -2.32 (0.19), residues: 2065 helix: -0.76 (0.28), residues: 373 sheet: -0.18 (0.24), residues: 494 loop : -2.52 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 479 HIS 0.003 0.001 HIS C 374 PHE 0.020 0.001 PHE H 102 TYR 0.010 0.001 TYR E 318 ARG 0.010 0.000 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 245 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 163 time to evaluate : 1.751 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: A 478 ASN cc_start: 0.7260 (p0) cc_final: 0.6255 (p0) REVERT: C 280 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7652 (m110) REVERT: E 280 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8194 (m110) REVERT: H 2 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.6908 (t) REVERT: H 3 GLN cc_start: 0.7208 (pm20) cc_final: 0.6922 (pm20) REVERT: H 82 MET cc_start: 0.8006 (mmm) cc_final: 0.7780 (mmm) REVERT: I 3 GLN cc_start: 0.7455 (pm20) cc_final: 0.6861 (pm20) REVERT: I 4 LEU cc_start: 0.7986 (tt) cc_final: 0.7737 (tp) REVERT: J 3 GLN cc_start: 0.7840 (pm20) cc_final: 0.7358 (pm20) outliers start: 82 outliers final: 49 residues processed: 237 average time/residue: 0.2767 time to fit residues: 100.9957 Evaluate side-chains 199 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 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 B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 127 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 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 202 THR 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 280 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 87 THR 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: 9.9990 chunk 180 optimal weight: 0.0970 chunk 39 optimal weight: 0.0970 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 0.0470 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 0.0060 overall best weight: 0.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 170 GLN ** E 188 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17825 Z= 0.172 Angle : 0.710 10.998 24181 Z= 0.348 Chirality : 0.046 0.257 2922 Planarity : 0.004 0.054 3009 Dihedral : 8.272 108.340 3829 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.35 % Favored : 90.22 % Rotamer: Outliers : 3.45 % Allowed : 31.63 % Favored : 64.91 % 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: -2.26 (0.19), residues: 2065 helix: -0.75 (0.28), residues: 364 sheet: -0.28 (0.25), residues: 465 loop : -2.35 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 479 HIS 0.002 0.001 HIS C 216 PHE 0.031 0.001 PHE H 27 TYR 0.027 0.001 TYR A 61 ARG 0.021 0.001 ARG F 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 246 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 183 time to evaluate : 1.937 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: A 150 MET cc_start: 0.7507 (mpp) cc_final: 0.7289 (mpp) REVERT: C 280 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7528 (m110) REVERT: C 478 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6657 (p0) REVERT: E 280 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8130 (m110) REVERT: H 2 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.7037 (t) REVERT: I 3 GLN cc_start: 0.7376 (pm20) cc_final: 0.6942 (pm20) REVERT: J 3 GLN cc_start: 0.7689 (pm20) cc_final: 0.7328 (pm20) outliers start: 63 outliers final: 45 residues processed: 238 average time/residue: 0.2812 time to fit residues: 104.0878 Evaluate side-chains 200 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 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 424 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 ASN 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 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 202 THR 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 280 ASN 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 448 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 THR 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: 3.9990 chunk 22 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 199 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** 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: 0.7912 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17825 Z= 0.264 Angle : 0.735 15.156 24181 Z= 0.361 Chirality : 0.045 0.255 2922 Planarity : 0.004 0.054 3009 Dihedral : 8.230 109.777 3828 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.56 % Favored : 88.96 % Rotamer: Outliers : 3.62 % Allowed : 32.13 % Favored : 64.25 % 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: -2.14 (0.19), residues: 2065 helix: -0.42 (0.29), residues: 346 sheet: -0.15 (0.25), residues: 470 loop : -2.36 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 479 HIS 0.003 0.001 HIS A 105 PHE 0.023 0.001 PHE H 102 TYR 0.016 0.001 TYR F 638 ARG 0.013 0.000 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 221 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 155 time to evaluate : 2.136 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: A 71 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 150 MET cc_start: 0.7582 (mpp) cc_final: 0.6907 (mpp) REVERT: C 280 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (m110) REVERT: E 150 MET cc_start: 0.8049 (mpp) cc_final: 0.7772 (mpp) REVERT: E 280 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8244 (m110) REVERT: I 3 GLN cc_start: 0.7609 (pm20) cc_final: 0.7111 (pm20) REVERT: J 3 GLN cc_start: 0.7638 (pm20) cc_final: 0.7295 (pm20) outliers start: 66 outliers final: 49 residues processed: 216 average time/residue: 0.2746 time to fit residues: 92.0273 Evaluate side-chains 200 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 71 THR 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 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 CYS 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 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE 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 89 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 202 THR 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 280 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 72 ASP 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: 0.0170 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3761 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= 0.177 Angle : 0.728 12.512 24181 Z= 0.353 Chirality : 0.045 0.248 2922 Planarity : 0.004 0.052 3009 Dihedral : 7.886 108.681 3828 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.44 % Favored : 90.12 % Rotamer: Outliers : 3.23 % Allowed : 32.46 % Favored : 64.31 % 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: -2.13 (0.19), residues: 2065 helix: -0.55 (0.29), residues: 361 sheet: -0.18 (0.25), residues: 470 loop : -2.31 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 479 HIS 0.002 0.001 HIS C 216 PHE 0.030 0.001 PHE J 27 TYR 0.017 0.001 TYR F 638 ARG 0.014 0.000 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 217 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 158 time to evaluate : 2.092 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 71 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 654 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 280 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (m110) REVERT: C 478 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6592 (p0) REVERT: E 280 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (m110) REVERT: H 3 GLN cc_start: 0.7353 (pm20) cc_final: 0.6856 (pm20) REVERT: I 3 GLN cc_start: 0.7585 (pm20) cc_final: 0.7173 (pm20) REVERT: J 3 GLN cc_start: 0.7619 (pm20) cc_final: 0.7282 (pm20) outliers start: 59 outliers final: 47 residues processed: 212 average time/residue: 0.2773 time to fit residues: 91.8716 Evaluate side-chains 201 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 150 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 71 THR 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 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 CYS 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 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 478 ASN 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 89 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 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 THR 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: 0.8980 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 168 optimal weight: 0.0070 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** 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: 0.7934 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17825 Z= 0.251 Angle : 0.739 11.859 24181 Z= 0.362 Chirality : 0.045 0.253 2922 Planarity : 0.004 0.053 3009 Dihedral : 7.855 107.812 3828 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.22 % Favored : 89.30 % Rotamer: Outliers : 3.29 % Allowed : 32.29 % Favored : 64.42 % 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: -2.10 (0.18), residues: 2065 helix: -0.23 (0.30), residues: 334 sheet: -0.03 (0.27), residues: 383 loop : -2.27 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 PHE 0.022 0.001 PHE H 102 TYR 0.016 0.001 TYR F 638 ARG 0.014 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 208 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 148 time to evaluate : 2.021 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: C 280 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7768 (m110) REVERT: E 280 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8228 (m110) REVERT: H 3 GLN cc_start: 0.7487 (pm20) cc_final: 0.7020 (pm20) REVERT: I 3 GLN cc_start: 0.7545 (pm20) cc_final: 0.7131 (pm20) REVERT: J 3 GLN cc_start: 0.7727 (pm20) cc_final: 0.7389 (pm20) outliers start: 60 outliers final: 50 residues processed: 203 average time/residue: 0.2737 time to fit residues: 86.4431 Evaluate side-chains 195 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 143 time to evaluate : 1.799 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 CYS 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 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 89 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 280 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 72 ASP 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 196 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 206 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 164 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** 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: 0.7886 moved from start: 0.4053 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= 0.177 Angle : 0.740 12.097 24181 Z= 0.358 Chirality : 0.045 0.246 2922 Planarity : 0.004 0.054 3009 Dihedral : 7.650 106.967 3828 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.49 % Favored : 90.07 % Rotamer: Outliers : 2.96 % Allowed : 32.51 % Favored : 64.53 % 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: -2.04 (0.19), residues: 2065 helix: -0.14 (0.30), residues: 334 sheet: -0.31 (0.25), residues: 468 loop : -2.23 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 PHE 0.032 0.001 PHE J 27 TYR 0.041 0.001 TYR C 61 ARG 0.015 0.001 ARG B 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 208 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 2.045 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: C 280 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7685 (m110) REVERT: E 280 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8029 (m110) REVERT: H 3 GLN cc_start: 0.7141 (pm20) cc_final: 0.6831 (pm20) REVERT: I 3 GLN cc_start: 0.7444 (pm20) cc_final: 0.7095 (pm20) REVERT: J 3 GLN cc_start: 0.7675 (pm20) cc_final: 0.7310 (pm20) outliers start: 54 outliers final: 47 residues processed: 203 average time/residue: 0.2768 time to fit residues: 87.4543 Evaluate side-chains 196 residues out of total 1825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 89 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 280 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 72 ASP 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: 4.9990 chunk 50 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 39 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.044585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.032738 restraints weight = 102045.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.034110 restraints weight = 56386.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.035101 restraints weight = 38808.509| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17825 Z= 0.261 Angle : 0.742 11.257 24181 Z= 0.362 Chirality : 0.045 0.253 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.718 105.352 3828 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.65 % Favored : 88.91 % Rotamer: Outliers : 3.18 % Allowed : 32.24 % Favored : 64.58 % 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: -2.07 (0.18), residues: 2065 helix: -0.09 (0.30), residues: 334 sheet: -0.08 (0.27), residues: 383 loop : -2.26 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 479 HIS 0.007 0.001 HIS E 105 PHE 0.022 0.001 PHE H 102 TYR 0.040 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: 3210.74 seconds wall clock time: 58 minutes 47.57 seconds (3527.57 seconds total)