Starting phenix.real_space_refine on Fri Mar 22 13:16:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnm_13549/03_2024/7pnm_13549.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnm_13549/03_2024/7pnm_13549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnm_13549/03_2024/7pnm_13549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnm_13549/03_2024/7pnm_13549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnm_13549/03_2024/7pnm_13549.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnm_13549/03_2024/7pnm_13549.pdb" } resolution = 3.7 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= 0.002 sd= 0.035 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 207 5.16 5 C 21303 2.51 5 N 5487 2.21 5 O 6543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33540 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.31, per 1000 atoms: 0.49 Number of scatterers: 33540 At special positions: 0 Unit cell: (191.7, 207.675, 161.88, 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 207 16.00 O 6543 8.00 N 5487 7.00 C 21303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.04 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 606 " distance=2.05 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 589 " distance=2.04 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 675 " distance=2.04 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 930 " - pdb=" SG CYS A 941 " distance=2.03 Simple disulfide: pdb=" SG CYS A1118 " - pdb=" SG CYS A1129 " distance=2.04 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 606 " distance=2.05 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 514 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 675 " distance=2.04 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 930 " - pdb=" SG CYS B 941 " distance=2.03 Simple disulfide: pdb=" SG CYS B1118 " - pdb=" SG CYS B1129 " distance=2.04 Simple disulfide: pdb=" SG CYS B1168 " - pdb=" SG CYS B1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.04 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 606 " distance=2.04 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 514 " distance=2.03 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 568 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 570 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 589 " distance=2.04 Simple disulfide: pdb=" SG CYS C 622 " - pdb=" SG CYS C 675 " distance=2.04 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 725 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 930 " - pdb=" SG CYS C 941 " distance=2.03 Simple disulfide: pdb=" SG CYS C1118 " - pdb=" SG CYS C1129 " distance=2.04 Simple disulfide: pdb=" SG CYS C1168 " - pdb=" SG CYS C1213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1401 " - " ASN A 441 " " NAG A1402 " - " ASN A 640 " " NAG A1403 " - " ASN A 731 " " NAG A1404 " - " ASN A 59 " " NAG A1405 " - " ASN A 146 " " NAG A1406 " - " ASN A 667 " " NAG A1407 " - " ASN A 687 " " NAG A1408 " - " ASN A 706 " " NAG B1401 " - " ASN B 441 " " NAG B1402 " - " ASN B 640 " " NAG B1403 " - " ASN B 731 " " NAG B1404 " - " ASN B 59 " " NAG B1405 " - " ASN B 146 " " NAG B1406 " - " ASN B 667 " " NAG B1407 " - " ASN B 687 " " NAG B1408 " - " ASN B 706 " " NAG C1401 " - " ASN C 441 " " NAG C1402 " - " ASN C 640 " " NAG C1403 " - " ASN C 731 " " NAG C1404 " - " ASN C 59 " " NAG C1405 " - " ASN C 146 " " NAG C1406 " - " ASN C 667 " " NAG C1407 " - " ASN C 687 " " NAG C1408 " - " ASN C 706 " " NAG F 1 " - " ASN A 133 " " NAG J 1 " - " ASN A 202 " " NAG K 1 " - " ASN A 363 " " NAG M 1 " - " ASN A 929 " " NAG N 1 " - " ASN B 133 " " NAG O 1 " - " ASN B 202 " " NAG P 1 " - " ASN B 363 " " NAG Q 1 " - " ASN B 929 " " NAG R 1 " - " ASN C 133 " " NAG S 1 " - " ASN C 202 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 929 " Time building additional restraints: 12.61 Conformation dependent library (CDL) restraints added in 6.5 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7854 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 84 sheets defined 21.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.563A pdb=" N TRP A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.765A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.598A pdb=" N LEU A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.507A pdb=" N LYS A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.718A pdb=" N VAL A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.627A pdb=" N PHE A 705 " --> pdb=" O CYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.990A pdb=" N VAL A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.717A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.676A pdb=" N GLY A 878 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.626A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 930 removed outlier: 4.095A pdb=" N CYS A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 946 removed outlier: 3.500A pdb=" N LYS A 946 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 973 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.793A pdb=" N SER A1003 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 Processing helix chain 'A' and resid 1028 through 1050 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1062 through 1070 Processing helix chain 'A' and resid 1071 through 1118 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.875A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.700A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.909A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.529A pdb=" N ASP H 104 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.591A pdb=" N TRP B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.769A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.600A pdb=" N LEU B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.506A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.747A pdb=" N VAL B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.605A pdb=" N PHE B 705 " --> pdb=" O CYS B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.977A pdb=" N VAL B 834 " --> pdb=" O LYS B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.737A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 878 removed outlier: 3.667A pdb=" N GLY B 878 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.570A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 930 removed outlier: 4.116A pdb=" N CYS B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 946 removed outlier: 3.506A pdb=" N LYS B 946 " --> pdb=" O VAL B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 973 Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 1000 through 1004 removed outlier: 3.834A pdb=" N SER B1003 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1023 Processing helix chain 'B' and resid 1028 through 1050 Processing helix chain 'B' and resid 1051 through 1053 No H-bonds generated for 'chain 'B' and resid 1051 through 1053' Processing helix chain 'B' and resid 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1118 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.892A pdb=" N VAL D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.718A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.877A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 105 removed outlier: 3.532A pdb=" N ASP G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 293 through 302 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.587A pdb=" N TRP C 340 " --> pdb=" O ASN C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.768A pdb=" N LEU C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.586A pdb=" N LEU C 409 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.548A pdb=" N LYS C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.733A pdb=" N VAL C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 700 through 708 removed outlier: 3.613A pdb=" N PHE C 705 " --> pdb=" O CYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 826 through 834 removed outlier: 3.988A pdb=" N VAL C 834 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.740A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.669A pdb=" N GLY C 878 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 915 removed outlier: 3.561A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 930 removed outlier: 4.071A pdb=" N CYS C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 946 removed outlier: 3.510A pdb=" N LYS C 946 " --> pdb=" O VAL C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 973 Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.799A pdb=" N SER C1003 " --> pdb=" O ASP C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 Processing helix chain 'C' and resid 1028 through 1050 Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1118 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.882A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.720A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.867A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 removed outlier: 3.525A pdb=" N ASP I 104 " --> pdb=" O GLN I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69 removed outlier: 4.604A pdb=" N GLU A 263 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 108 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 237 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.845A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.195A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.761A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 161 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 199 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.761A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313 removed outlier: 3.901A pdb=" N PHE A 684 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AB1, first strand: chain 'A' and resid 323 through 327 removed outlier: 3.677A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 659 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.784A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 398 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 396 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 375 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.784A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 398 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 396 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AB5, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AB6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.327A pdb=" N CYS A 483 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 543 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AB8, first strand: chain 'A' and resid 730 through 737 removed outlier: 7.373A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 777 through 779 removed outlier: 5.819A pdb=" N ASN A 777 " --> pdb=" O LEU B 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 790 through 800 removed outlier: 3.698A pdb=" N ILE A 792 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1161 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 790 through 800 removed outlier: 3.698A pdb=" N ILE A 792 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1161 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A1145 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1142 " --> pdb=" O GLY A1145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 814 through 816 Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 872 Processing sheet with id=AC5, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.544A pdb=" N VAL A 883 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1207 through 1210 removed outlier: 3.698A pdb=" N ALA A1176 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1181 through 1185 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.625A pdb=" N VAL L 13 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN L 43 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET L 94 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 39 " --> pdb=" O MET L 94 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.268A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.253A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD4, first strand: chain 'B' and resid 61 through 69 removed outlier: 4.585A pdb=" N GLU B 263 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 108 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 217 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.783A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 81 through 82 removed outlier: 8.372A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.764A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 161 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 199 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.764A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AE1, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.862A pdb=" N PHE B 684 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 681 " --> pdb=" O LEU B 694 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 323 through 327 removed outlier: 3.732A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B 659 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.837A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 396 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 430 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 375 " --> pdb=" O TYR B 434 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.837A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 396 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AE6, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AE7, first strand: chain 'B' and resid 483 through 485 removed outlier: 4.272A pdb=" N CYS B 483 " --> pdb=" O SER B 545 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 543 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AE9, first strand: chain 'B' and resid 730 through 737 removed outlier: 7.322A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 777 through 779 removed outlier: 5.825A pdb=" N ASN B 777 " --> pdb=" O LEU C 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 790 through 800 removed outlier: 3.718A pdb=" N ILE B 792 " --> pdb=" O ALA B1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1161 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 790 through 800 removed outlier: 3.718A pdb=" N ILE B 792 " --> pdb=" O ALA B1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1161 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AF5, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.550A pdb=" N VAL B 883 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1207 through 1210 removed outlier: 3.679A pdb=" N ALA B1176 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1167 " --> pdb=" O ILE B1175 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1181 through 1185 Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.641A pdb=" N VAL D 13 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 90 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 43 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET D 94 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP D 39 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.287A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.516A pdb=" N THR G 118 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 117 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 50 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR G 59 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AG4, first strand: chain 'C' and resid 61 through 69 removed outlier: 4.642A pdb=" N GLU C 263 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 108 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.753A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 81 through 82 removed outlier: 8.374A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.755A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 161 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 199 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.755A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AH1, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.883A pdb=" N PHE C 684 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.550A pdb=" N TYR C 317 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 678 " --> pdb=" O TYR C 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'C' and resid 323 through 327 removed outlier: 3.720A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR C 659 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.776A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 398 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 430 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 375 " --> pdb=" O TYR C 434 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.170A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 361 through 362 Processing sheet with id=AH7, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AH8, first strand: chain 'C' and resid 483 through 485 removed outlier: 4.325A pdb=" N CYS C 483 " --> pdb=" O SER C 545 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 543 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AI1, first strand: chain 'C' and resid 730 through 737 removed outlier: 7.307A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN C 770 " --> pdb=" O TYR C 730 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N SER C 732 " --> pdb=" O ASN C 770 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 790 through 800 removed outlier: 3.728A pdb=" N ILE C 792 " --> pdb=" O ALA C1161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1161 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 790 through 800 removed outlier: 3.728A pdb=" N ILE C 792 " --> pdb=" O ALA C1161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1161 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 814 through 816 Processing sheet with id=AI5, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.544A pdb=" N VAL C 883 " --> pdb=" O ILE C 886 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 1167 through 1168 Processing sheet with id=AI7, first strand: chain 'C' and resid 1174 through 1177 removed outlier: 3.647A pdb=" N ALA C1176 " --> pdb=" O VAL C1208 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 1181 through 1185 Processing sheet with id=AI9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.652A pdb=" N VAL E 13 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 90 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 43 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 94 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP E 39 " --> pdb=" O MET E 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AJ2, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.279A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU I 20 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR I 118 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 50 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR I 59 " --> pdb=" O VAL I 50 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3411 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: 16.00 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10653 1.34 - 1.47: 8740 1.47 - 1.59: 14630 1.59 - 1.72: 0 1.72 - 1.84: 273 Bond restraints: 34296 Sorted by residual: bond pdb=" C1 NAG C1404 " pdb=" O5 NAG C1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 NAG B1404 " pdb=" O5 NAG B1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 34291 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.69: 662 105.69 - 112.80: 17949 112.80 - 119.92: 11681 119.92 - 127.03: 16067 127.03 - 134.14: 318 Bond angle restraints: 46677 Sorted by residual: angle pdb=" N GLN B 860 " pdb=" CA GLN B 860 " pdb=" CB GLN B 860 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLN A 860 " pdb=" CA GLN A 860 " pdb=" CB GLN A 860 " ideal model delta sigma weight residual 110.16 116.17 -6.01 1.48e+00 4.57e-01 1.65e+01 angle pdb=" C ASN B1186 " pdb=" N ASN B1187 " pdb=" CA ASN B1187 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C ASN C1186 " pdb=" N ASN C1187 " pdb=" CA ASN C1187 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 ... (remaining 46672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 19813 23.53 - 47.05: 1049 47.05 - 70.58: 102 70.58 - 94.11: 33 94.11 - 117.63: 9 Dihedral angle restraints: 21006 sinusoidal: 8703 harmonic: 12303 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 197 " pdb=" CB CYS A 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.11 59.89 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS B 164 " pdb=" SG CYS B 164 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.14 59.86 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 197 " pdb=" CB CYS C 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.75 59.25 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 21003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4574 0.074 - 0.149: 738 0.149 - 0.223: 58 0.223 - 0.297: 3 0.297 - 0.371: 3 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1 NAG A1405 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A1405 " pdb=" O5 NAG A1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 5373 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 772 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO C 773 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 773 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 773 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 92 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 93 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 92 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 93 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.026 5.00e-02 4.00e+02 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8672 2.80 - 3.32: 27854 3.32 - 3.85: 55776 3.85 - 4.37: 62158 4.37 - 4.90: 109433 Nonbonded interactions: 263893 Sorted by model distance: nonbonded pdb=" O GLU C 852 " pdb=" OG1 THR C 856 " model vdw 2.275 2.440 nonbonded pdb=" O GLU B 852 " pdb=" OG1 THR B 856 " model vdw 2.278 2.440 nonbonded pdb=" O GLU A 852 " pdb=" OG1 THR A 856 " model vdw 2.287 2.440 nonbonded pdb=" OD2 ASP A 397 " pdb=" OH TYR A 422 " model vdw 2.291 2.440 nonbonded pdb=" OD2 ASP B 397 " pdb=" OH TYR B 422 " model vdw 2.296 2.440 ... (remaining 263888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.560 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 86.070 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 34296 Z= 0.258 Angle : 0.752 12.521 46677 Z= 0.393 Chirality : 0.053 0.371 5376 Planarity : 0.005 0.048 5952 Dihedral : 13.599 117.634 12945 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 4176 helix: -1.65 (0.16), residues: 750 sheet: -0.88 (0.16), residues: 981 loop : -1.54 (0.11), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.006 0.001 HIS H 35 PHE 0.018 0.001 PHE A 122 TYR 0.028 0.002 TYR B 317 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 944 time to evaluate : 4.123 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 78 MET cc_start: 0.7116 (mmm) cc_final: 0.6843 (tpt) REVERT: A 180 LEU cc_start: 0.8557 (mt) cc_final: 0.8246 (mt) REVERT: A 259 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7435 (ptmt) REVERT: A 315 ASN cc_start: 0.7542 (p0) cc_final: 0.7304 (p0) REVERT: A 329 LYS cc_start: 0.7537 (mmmm) cc_final: 0.7328 (ttmm) REVERT: A 425 ASP cc_start: 0.7202 (t70) cc_final: 0.6924 (t0) REVERT: A 437 LEU cc_start: 0.8001 (mt) cc_final: 0.7513 (mt) REVERT: A 626 ASP cc_start: 0.6826 (t0) cc_final: 0.6348 (t0) REVERT: A 1000 ASP cc_start: 0.7427 (t0) cc_final: 0.6994 (t0) REVERT: A 1005 ASN cc_start: 0.7344 (t0) cc_final: 0.7022 (t0) REVERT: A 1035 GLN cc_start: 0.7499 (tp40) cc_final: 0.7243 (tp40) REVERT: A 1060 SER cc_start: 0.7642 (t) cc_final: 0.7421 (t) REVERT: A 1079 ILE cc_start: 0.7571 (mt) cc_final: 0.7043 (mt) REVERT: A 1087 LEU cc_start: 0.7615 (mt) cc_final: 0.7192 (mt) REVERT: A 1182 PHE cc_start: 0.7508 (m-80) cc_final: 0.7206 (m-80) REVERT: A 1187 ASN cc_start: 0.8835 (p0) cc_final: 0.8630 (p0) REVERT: L 75 ASP cc_start: 0.7330 (p0) cc_final: 0.6712 (m-30) REVERT: H 103 LEU cc_start: 0.8925 (tp) cc_final: 0.8207 (tt) REVERT: B 29 LYS cc_start: 0.7540 (tptt) cc_final: 0.7118 (ttpp) REVERT: B 78 MET cc_start: 0.7007 (mmm) cc_final: 0.6699 (tpt) REVERT: B 106 LYS cc_start: 0.6938 (tptp) cc_final: 0.6607 (ttmm) REVERT: B 180 LEU cc_start: 0.8530 (mt) cc_final: 0.8238 (mt) REVERT: B 235 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7412 (mtmm) REVERT: B 259 LYS cc_start: 0.7648 (ptmt) cc_final: 0.7300 (ptmt) REVERT: B 423 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: B 437 LEU cc_start: 0.7816 (mt) cc_final: 0.7500 (mt) REVERT: B 478 VAL cc_start: 0.8206 (p) cc_final: 0.7853 (m) REVERT: B 596 ILE cc_start: 0.8737 (mm) cc_final: 0.8205 (mm) REVERT: B 597 LEU cc_start: 0.8472 (mt) cc_final: 0.8239 (mt) REVERT: B 626 ASP cc_start: 0.7021 (t0) cc_final: 0.6473 (t0) REVERT: B 662 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.7041 (mtp-110) REVERT: B 668 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7287 (mtm-85) REVERT: B 697 ASN cc_start: 0.7013 (m-40) cc_final: 0.6695 (m-40) REVERT: B 720 ASP cc_start: 0.7295 (m-30) cc_final: 0.6661 (m-30) REVERT: B 808 GLN cc_start: 0.6900 (pt0) cc_final: 0.6582 (pt0) REVERT: B 923 PHE cc_start: 0.7519 (m-80) cc_final: 0.6991 (m-80) REVERT: B 958 ASN cc_start: 0.7404 (m110) cc_final: 0.7023 (m-40) REVERT: B 963 TYR cc_start: 0.7486 (m-10) cc_final: 0.7161 (m-80) REVERT: B 1035 GLN cc_start: 0.7703 (tp40) cc_final: 0.7499 (tp40) REVERT: B 1039 ASN cc_start: 0.7666 (t0) cc_final: 0.7399 (t0) REVERT: B 1079 ILE cc_start: 0.7544 (mt) cc_final: 0.7288 (mt) REVERT: B 1087 LEU cc_start: 0.7457 (mt) cc_final: 0.6937 (mt) REVERT: B 1126 ILE cc_start: 0.8188 (mm) cc_final: 0.7944 (mm) REVERT: B 1139 VAL cc_start: 0.8449 (t) cc_final: 0.8016 (p) REVERT: B 1141 ASN cc_start: 0.8094 (t0) cc_final: 0.7792 (t0) REVERT: B 1182 PHE cc_start: 0.7531 (m-80) cc_final: 0.7144 (m-80) REVERT: B 1198 TYR cc_start: 0.7070 (t80) cc_final: 0.6860 (t80) REVERT: D 75 ASP cc_start: 0.7267 (p0) cc_final: 0.6877 (m-30) REVERT: G 103 LEU cc_start: 0.8938 (tp) cc_final: 0.8422 (tt) REVERT: G 105 TYR cc_start: 0.5107 (t80) cc_final: 0.4853 (t80) REVERT: C 29 LYS cc_start: 0.7446 (tptt) cc_final: 0.7082 (ttpp) REVERT: C 78 MET cc_start: 0.6854 (mmm) cc_final: 0.6517 (tpp) REVERT: C 180 LEU cc_start: 0.8471 (mt) cc_final: 0.8174 (mp) REVERT: C 237 LEU cc_start: 0.7747 (tp) cc_final: 0.7506 (tp) REVERT: C 259 LYS cc_start: 0.7625 (ptmt) cc_final: 0.7310 (ptmt) REVERT: C 344 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7630 (ttmm) REVERT: C 382 ASP cc_start: 0.7507 (p0) cc_final: 0.7220 (p0) REVERT: C 422 TYR cc_start: 0.7138 (t80) cc_final: 0.6774 (t80) REVERT: C 425 ASP cc_start: 0.7126 (t70) cc_final: 0.6898 (t0) REVERT: C 461 ASP cc_start: 0.7154 (p0) cc_final: 0.6921 (p0) REVERT: C 478 VAL cc_start: 0.8435 (p) cc_final: 0.8112 (m) REVERT: C 596 ILE cc_start: 0.8820 (mm) cc_final: 0.8536 (mm) REVERT: C 689 SER cc_start: 0.7227 (t) cc_final: 0.7003 (t) REVERT: C 799 THR cc_start: 0.7556 (t) cc_final: 0.7346 (t) REVERT: C 855 ASP cc_start: 0.6530 (p0) cc_final: 0.6224 (p0) REVERT: C 1000 ASP cc_start: 0.7408 (t0) cc_final: 0.7177 (t0) REVERT: C 1039 ASN cc_start: 0.7579 (t0) cc_final: 0.7195 (t0) REVERT: C 1073 LEU cc_start: 0.6491 (pt) cc_final: 0.6170 (pt) REVERT: C 1079 ILE cc_start: 0.7612 (mt) cc_final: 0.7407 (mt) REVERT: C 1106 PHE cc_start: 0.6753 (t80) cc_final: 0.6409 (t80) REVERT: C 1154 VAL cc_start: 0.7880 (t) cc_final: 0.7670 (p) REVERT: C 1182 PHE cc_start: 0.7427 (m-80) cc_final: 0.7165 (m-80) REVERT: E 21 ILE cc_start: 0.8619 (mt) cc_final: 0.8414 (tp) REVERT: I 103 LEU cc_start: 0.8745 (tp) cc_final: 0.8449 (tt) outliers start: 5 outliers final: 0 residues processed: 949 average time/residue: 0.4583 time to fit residues: 722.0629 Evaluate side-chains 830 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 830 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 5.9990 chunk 318 optimal weight: 0.0040 chunk 176 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 170 optimal weight: 0.0000 chunk 329 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 381 optimal weight: 0.7980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 657 ASN A 697 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 GLN A1110 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 697 ASN B 777 ASN B 844 ASN B 928 ASN B1096 GLN B1150 HIS D 47 GLN G 13 GLN C 410 GLN C 657 ASN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 GLN C1096 GLN E 47 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34296 Z= 0.283 Angle : 0.641 8.388 46677 Z= 0.337 Chirality : 0.048 0.378 5376 Planarity : 0.004 0.042 5952 Dihedral : 7.714 103.852 5592 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.05 % Allowed : 9.56 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 4176 helix: -0.51 (0.18), residues: 765 sheet: -0.73 (0.16), residues: 975 loop : -1.32 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 102 HIS 0.008 0.001 HIS B 215 PHE 0.027 0.002 PHE C 203 TYR 0.024 0.002 TYR C1191 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 883 time to evaluate : 2.911 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 180 LEU cc_start: 0.8501 (mt) cc_final: 0.8248 (mt) REVERT: A 259 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7382 (ptmt) REVERT: A 328 ARG cc_start: 0.6981 (mpt180) cc_final: 0.6732 (mpt180) REVERT: A 342 ASN cc_start: 0.7526 (t0) cc_final: 0.7093 (t0) REVERT: A 343 ASP cc_start: 0.7032 (t0) cc_final: 0.6818 (t0) REVERT: A 345 SER cc_start: 0.7835 (p) cc_final: 0.7630 (m) REVERT: A 375 SER cc_start: 0.7835 (t) cc_final: 0.7384 (m) REVERT: A 425 ASP cc_start: 0.7205 (t70) cc_final: 0.6904 (t0) REVERT: A 478 VAL cc_start: 0.8456 (p) cc_final: 0.8123 (m) REVERT: A 610 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 626 ASP cc_start: 0.6821 (t0) cc_final: 0.6378 (t0) REVERT: A 663 ASP cc_start: 0.7194 (t70) cc_final: 0.6959 (t70) REVERT: A 832 GLN cc_start: 0.7713 (mm110) cc_final: 0.7433 (mm110) REVERT: A 850 VAL cc_start: 0.7941 (m) cc_final: 0.7676 (p) REVERT: A 858 GLN cc_start: 0.6647 (mm110) cc_final: 0.6285 (mm-40) REVERT: A 1000 ASP cc_start: 0.7465 (t0) cc_final: 0.7158 (t0) REVERT: A 1065 GLU cc_start: 0.5159 (mt-10) cc_final: 0.4857 (mt-10) REVERT: A 1076 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5862 (tt0) REVERT: A 1182 PHE cc_start: 0.7317 (m-80) cc_final: 0.7073 (m-80) REVERT: A 1190 MET cc_start: 0.6834 (ttt) cc_final: 0.6286 (ttt) REVERT: A 1200 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6861 (tt0) REVERT: L 31 HIS cc_start: 0.7372 (t-170) cc_final: 0.7163 (t-170) REVERT: L 41 TYR cc_start: 0.8521 (m-10) cc_final: 0.8138 (m-10) REVERT: H 52 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.6202 (t-100) REVERT: H 103 LEU cc_start: 0.8994 (tp) cc_final: 0.8207 (tt) REVERT: B 30 ASP cc_start: 0.7664 (t0) cc_final: 0.7409 (t0) REVERT: B 78 MET cc_start: 0.7209 (mmm) cc_final: 0.6940 (tpt) REVERT: B 106 LYS cc_start: 0.6949 (tptp) cc_final: 0.6661 (tttp) REVERT: B 235 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7598 (mtmm) REVERT: B 241 TYR cc_start: 0.7101 (t80) cc_final: 0.6879 (t80) REVERT: B 259 LYS cc_start: 0.7669 (ptmt) cc_final: 0.7281 (ptmt) REVERT: B 315 ASN cc_start: 0.7762 (p0) cc_final: 0.7480 (p0) REVERT: B 326 TYR cc_start: 0.7399 (t80) cc_final: 0.7100 (t80) REVERT: B 328 ARG cc_start: 0.6987 (mpt180) cc_final: 0.6766 (mpt180) REVERT: B 344 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7649 (ttmm) REVERT: B 382 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7109 (p0) REVERT: B 405 ARG cc_start: 0.7456 (mmm160) cc_final: 0.7111 (tpp-160) REVERT: B 460 GLU cc_start: 0.7610 (mp0) cc_final: 0.7405 (mp0) REVERT: B 478 VAL cc_start: 0.8404 (p) cc_final: 0.8054 (m) REVERT: B 627 LEU cc_start: 0.8657 (mt) cc_final: 0.8408 (mt) REVERT: B 689 SER cc_start: 0.7588 (t) cc_final: 0.7365 (t) REVERT: B 716 ILE cc_start: 0.7770 (mp) cc_final: 0.7500 (mp) REVERT: B 772 GLU cc_start: 0.6996 (tp30) cc_final: 0.6793 (tp30) REVERT: B 858 GLN cc_start: 0.6794 (mm110) cc_final: 0.6526 (mm110) REVERT: B 923 PHE cc_start: 0.7693 (m-80) cc_final: 0.7394 (m-80) REVERT: B 928 ASN cc_start: 0.7229 (m-40) cc_final: 0.6984 (m110) REVERT: B 951 LEU cc_start: 0.8521 (mm) cc_final: 0.8206 (mt) REVERT: B 958 ASN cc_start: 0.7568 (m110) cc_final: 0.7174 (m-40) REVERT: B 963 TYR cc_start: 0.7693 (m-10) cc_final: 0.7032 (m-80) REVERT: B 1112 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6413 (mpp) REVERT: B 1113 GLU cc_start: 0.6754 (tt0) cc_final: 0.6465 (tt0) REVERT: B 1139 VAL cc_start: 0.8487 (t) cc_final: 0.8097 (p) REVERT: B 1141 ASN cc_start: 0.8228 (t0) cc_final: 0.7970 (t0) REVERT: B 1181 TYR cc_start: 0.7402 (m-80) cc_final: 0.7180 (m-10) REVERT: B 1182 PHE cc_start: 0.7315 (m-80) cc_final: 0.6949 (m-80) REVERT: B 1183 VAL cc_start: 0.7930 (t) cc_final: 0.7531 (m) REVERT: B 1189 TRP cc_start: 0.8432 (m100) cc_final: 0.8171 (m100) REVERT: B 1190 MET cc_start: 0.6958 (ttm) cc_final: 0.6487 (ttt) REVERT: D 75 ASP cc_start: 0.7423 (p0) cc_final: 0.7079 (m-30) REVERT: G 52 TRP cc_start: 0.6760 (OUTLIER) cc_final: 0.6077 (t-100) REVERT: G 102 TRP cc_start: 0.7651 (p-90) cc_final: 0.7349 (p-90) REVERT: C 180 LEU cc_start: 0.8549 (mt) cc_final: 0.8250 (mp) REVERT: C 235 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7445 (mtmm) REVERT: C 241 TYR cc_start: 0.6991 (t80) cc_final: 0.6744 (t80) REVERT: C 259 LYS cc_start: 0.7590 (ptmt) cc_final: 0.7278 (ptmt) REVERT: C 325 VAL cc_start: 0.7531 (p) cc_final: 0.7326 (m) REVERT: C 326 TYR cc_start: 0.7360 (t80) cc_final: 0.7060 (t80) REVERT: C 328 ARG cc_start: 0.6579 (mpt180) cc_final: 0.6316 (mpt180) REVERT: C 342 ASN cc_start: 0.8012 (t0) cc_final: 0.7604 (t0) REVERT: C 422 TYR cc_start: 0.7266 (t80) cc_final: 0.6981 (t80) REVERT: C 460 GLU cc_start: 0.7797 (mp0) cc_final: 0.7544 (mp0) REVERT: C 478 VAL cc_start: 0.8384 (p) cc_final: 0.8128 (m) REVERT: C 494 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7676 (mmmt) REVERT: C 626 ASP cc_start: 0.6674 (t0) cc_final: 0.6344 (t0) REVERT: C 662 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.7370 (mtm110) REVERT: C 699 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7478 (mtmm) REVERT: C 738 GLN cc_start: 0.7310 (mm110) cc_final: 0.6947 (mm110) REVERT: C 832 GLN cc_start: 0.7983 (mm110) cc_final: 0.7327 (mp10) REVERT: C 999 MET cc_start: 0.6663 (ttp) cc_final: 0.6148 (mtp) REVERT: C 1005 ASN cc_start: 0.7340 (t0) cc_final: 0.6993 (t0) REVERT: C 1039 ASN cc_start: 0.7871 (t0) cc_final: 0.7404 (t0) REVERT: C 1069 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6854 (mtm-85) REVERT: C 1182 PHE cc_start: 0.7254 (m-80) cc_final: 0.6988 (m-80) REVERT: C 1190 MET cc_start: 0.6462 (ttt) cc_final: 0.5834 (ttt) REVERT: E 54 TYR cc_start: 0.7350 (p90) cc_final: 0.7128 (p90) REVERT: I 103 LEU cc_start: 0.8948 (tp) cc_final: 0.8469 (tt) outliers start: 75 outliers final: 44 residues processed: 903 average time/residue: 0.4294 time to fit residues: 630.1207 Evaluate side-chains 880 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 830 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 317 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 382 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 378 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 306 optimal weight: 0.0370 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 624 ASN A 697 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 GLN ** A1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN B 410 GLN B 697 ASN B 844 ASN B1091 ASN B1134 HIS B1150 HIS ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 GLN ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 34296 Z= 0.238 Angle : 0.609 8.632 46677 Z= 0.319 Chirality : 0.046 0.349 5376 Planarity : 0.004 0.040 5952 Dihedral : 7.218 101.951 5592 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.68 % Allowed : 12.65 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4176 helix: -0.09 (0.18), residues: 753 sheet: -0.70 (0.16), residues: 1038 loop : -1.17 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 102 HIS 0.006 0.001 HIS A 215 PHE 0.018 0.002 PHE A 227 TYR 0.025 0.002 TYR B1093 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 875 time to evaluate : 4.029 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: A 43 VAL cc_start: 0.7408 (m) cc_final: 0.6937 (t) REVERT: A 50 TYR cc_start: 0.6951 (p90) cc_final: 0.6710 (p90) REVERT: A 180 LEU cc_start: 0.8510 (mt) cc_final: 0.8303 (mp) REVERT: A 315 ASN cc_start: 0.7426 (p0) cc_final: 0.7039 (p0) REVERT: A 328 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6743 (mpt180) REVERT: A 342 ASN cc_start: 0.7739 (t0) cc_final: 0.7172 (t0) REVERT: A 345 SER cc_start: 0.8022 (p) cc_final: 0.7729 (m) REVERT: A 375 SER cc_start: 0.7786 (t) cc_final: 0.7347 (m) REVERT: A 425 ASP cc_start: 0.7340 (t70) cc_final: 0.7032 (t0) REVERT: A 437 LEU cc_start: 0.7893 (mt) cc_final: 0.7575 (mt) REVERT: A 478 VAL cc_start: 0.8478 (p) cc_final: 0.8180 (m) REVERT: A 596 ILE cc_start: 0.8767 (mm) cc_final: 0.8442 (mt) REVERT: A 598 HIS cc_start: 0.7709 (m90) cc_final: 0.7425 (m90) REVERT: A 610 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 626 ASP cc_start: 0.6761 (t0) cc_final: 0.6415 (t0) REVERT: A 832 GLN cc_start: 0.7718 (mm110) cc_final: 0.7501 (mm110) REVERT: A 850 VAL cc_start: 0.7933 (m) cc_final: 0.7706 (p) REVERT: A 858 GLN cc_start: 0.6633 (mm110) cc_final: 0.6396 (mm-40) REVERT: A 859 LEU cc_start: 0.8332 (mt) cc_final: 0.7974 (mt) REVERT: A 960 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: A 1000 ASP cc_start: 0.7441 (t0) cc_final: 0.7125 (t0) REVERT: A 1076 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: A 1112 MET cc_start: 0.7161 (mmm) cc_final: 0.6881 (mmm) REVERT: A 1177 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7635 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7302 (m-80) cc_final: 0.6656 (m-80) REVERT: A 1190 MET cc_start: 0.6962 (ttt) cc_final: 0.6458 (ttt) REVERT: A 1198 TYR cc_start: 0.7273 (t80) cc_final: 0.6850 (t80) REVERT: L 4 MET cc_start: 0.5178 (mpp) cc_final: 0.4895 (mpp) REVERT: H 52 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.6235 (t-100) REVERT: H 103 LEU cc_start: 0.9012 (tp) cc_final: 0.8245 (tt) REVERT: B 78 MET cc_start: 0.7232 (mmm) cc_final: 0.7022 (tpp) REVERT: B 235 LYS cc_start: 0.7834 (mtmm) cc_final: 0.7566 (mtmm) REVERT: B 259 LYS cc_start: 0.7622 (ptmt) cc_final: 0.7251 (ptmt) REVERT: B 368 MET cc_start: 0.7047 (ptp) cc_final: 0.6770 (ptm) REVERT: B 382 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7288 (p0) REVERT: B 395 THR cc_start: 0.8156 (m) cc_final: 0.7868 (p) REVERT: B 460 GLU cc_start: 0.7565 (mp0) cc_final: 0.7341 (mp0) REVERT: B 478 VAL cc_start: 0.8437 (p) cc_final: 0.8176 (m) REVERT: B 626 ASP cc_start: 0.7067 (t0) cc_final: 0.6480 (t0) REVERT: B 689 SER cc_start: 0.7579 (t) cc_final: 0.7335 (t) REVERT: B 699 LYS cc_start: 0.7629 (mmmm) cc_final: 0.7103 (mmmm) REVERT: B 749 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.4953 (t) REVERT: B 772 GLU cc_start: 0.6855 (tp30) cc_final: 0.6615 (tp30) REVERT: B 858 GLN cc_start: 0.6683 (mm110) cc_final: 0.6437 (mm110) REVERT: B 923 PHE cc_start: 0.7538 (m-80) cc_final: 0.7333 (m-80) REVERT: B 951 LEU cc_start: 0.8496 (mm) cc_final: 0.8187 (mt) REVERT: B 958 ASN cc_start: 0.7579 (m110) cc_final: 0.7199 (m-40) REVERT: B 1000 ASP cc_start: 0.7535 (t0) cc_final: 0.7184 (t0) REVERT: B 1112 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6436 (mpp) REVERT: B 1139 VAL cc_start: 0.8433 (t) cc_final: 0.8047 (p) REVERT: B 1141 ASN cc_start: 0.8218 (t0) cc_final: 0.7988 (t0) REVERT: B 1182 PHE cc_start: 0.7480 (m-80) cc_final: 0.7118 (m-80) REVERT: B 1189 TRP cc_start: 0.8461 (m100) cc_final: 0.8189 (m100) REVERT: B 1190 MET cc_start: 0.6999 (ttm) cc_final: 0.6598 (ttt) REVERT: D 75 ASP cc_start: 0.7451 (p0) cc_final: 0.7097 (m-30) REVERT: G 52 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.5741 (t-100) REVERT: G 102 TRP cc_start: 0.7729 (p-90) cc_final: 0.7289 (p-90) REVERT: G 103 LEU cc_start: 0.9046 (tp) cc_final: 0.8678 (tp) REVERT: C 180 LEU cc_start: 0.8606 (mt) cc_final: 0.8280 (mp) REVERT: C 235 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7436 (mtmm) REVERT: C 241 TYR cc_start: 0.6987 (t80) cc_final: 0.6700 (t80) REVERT: C 259 LYS cc_start: 0.7630 (ptmt) cc_final: 0.7380 (ptmt) REVERT: C 279 ASN cc_start: 0.7744 (p0) cc_final: 0.7543 (p0) REVERT: C 325 VAL cc_start: 0.7612 (p) cc_final: 0.7400 (m) REVERT: C 328 ARG cc_start: 0.6507 (mpt180) cc_final: 0.6132 (mpt180) REVERT: C 342 ASN cc_start: 0.8082 (t0) cc_final: 0.7718 (t0) REVERT: C 478 VAL cc_start: 0.8357 (p) cc_final: 0.8098 (m) REVERT: C 494 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7763 (mmmt) REVERT: C 544 LYS cc_start: 0.6526 (mmmt) cc_final: 0.6326 (mmmm) REVERT: C 626 ASP cc_start: 0.6527 (t0) cc_final: 0.5837 (t0) REVERT: C 662 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7387 (mtm110) REVERT: C 680 VAL cc_start: 0.8519 (t) cc_final: 0.8196 (m) REVERT: C 699 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7571 (mtmm) REVERT: C 738 GLN cc_start: 0.7520 (mm110) cc_final: 0.7214 (mm-40) REVERT: C 832 GLN cc_start: 0.8018 (mm110) cc_final: 0.7259 (mp10) REVERT: C 858 GLN cc_start: 0.6382 (mm110) cc_final: 0.6130 (mm110) REVERT: C 921 VAL cc_start: 0.7968 (m) cc_final: 0.7353 (m) REVERT: C 986 LEU cc_start: 0.7761 (mt) cc_final: 0.7552 (mt) REVERT: C 1005 ASN cc_start: 0.7343 (t0) cc_final: 0.7025 (t0) REVERT: C 1039 ASN cc_start: 0.7735 (t0) cc_final: 0.7508 (t0) REVERT: C 1177 PRO cc_start: 0.8146 (Cg_endo) cc_final: 0.7517 (Cg_exo) REVERT: C 1182 PHE cc_start: 0.7324 (m-80) cc_final: 0.6673 (m-80) REVERT: C 1190 MET cc_start: 0.6773 (ttt) cc_final: 0.6150 (ttt) REVERT: E 42 LEU cc_start: 0.6507 (mt) cc_final: 0.6214 (mt) REVERT: E 84 GLU cc_start: 0.6658 (pp20) cc_final: 0.5915 (pp20) REVERT: I 103 LEU cc_start: 0.8980 (tp) cc_final: 0.8438 (tt) outliers start: 98 outliers final: 57 residues processed: 910 average time/residue: 0.4407 time to fit residues: 658.6114 Evaluate side-chains 913 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 848 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1127 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 10.0000 chunk 287 optimal weight: 0.0040 chunk 198 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 256 optimal weight: 40.0000 chunk 383 optimal weight: 3.9990 chunk 405 optimal weight: 9.9990 chunk 200 optimal weight: 0.7980 chunk 363 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A1096 GLN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN B 410 GLN B 697 ASN B 844 ASN B 860 GLN B1091 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS G 13 GLN C 173 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34296 Z= 0.210 Angle : 0.590 9.024 46677 Z= 0.306 Chirality : 0.046 0.344 5376 Planarity : 0.003 0.038 5952 Dihedral : 6.740 98.862 5592 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.79 % Allowed : 14.95 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4176 helix: 0.16 (0.19), residues: 750 sheet: -0.60 (0.16), residues: 1062 loop : -1.15 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 102 HIS 0.006 0.001 HIS H 35 PHE 0.019 0.001 PHE C 214 TYR 0.023 0.002 TYR C 435 ARG 0.007 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 871 time to evaluate : 3.426 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: A 297 GLU cc_start: 0.5818 (tt0) cc_final: 0.5604 (tt0) REVERT: A 315 ASN cc_start: 0.7435 (p0) cc_final: 0.7058 (p0) REVERT: A 342 ASN cc_start: 0.7775 (t0) cc_final: 0.7171 (t0) REVERT: A 375 SER cc_start: 0.7763 (t) cc_final: 0.7335 (m) REVERT: A 425 ASP cc_start: 0.7292 (t70) cc_final: 0.6996 (t0) REVERT: A 437 LEU cc_start: 0.7878 (mt) cc_final: 0.7652 (mt) REVERT: A 478 VAL cc_start: 0.8462 (p) cc_final: 0.8176 (m) REVERT: A 573 GLN cc_start: 0.7610 (mp10) cc_final: 0.7359 (mp10) REVERT: A 596 ILE cc_start: 0.8690 (mm) cc_final: 0.8426 (mt) REVERT: A 610 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8345 (pp) REVERT: A 626 ASP cc_start: 0.6771 (t0) cc_final: 0.6460 (t0) REVERT: A 731 ASN cc_start: 0.7509 (t0) cc_final: 0.6957 (t0) REVERT: A 766 TYR cc_start: 0.7054 (m-80) cc_final: 0.6777 (m-10) REVERT: A 832 GLN cc_start: 0.7681 (mm110) cc_final: 0.7473 (mm110) REVERT: A 960 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: A 1000 ASP cc_start: 0.7396 (t0) cc_final: 0.7122 (t0) REVERT: A 1076 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5974 (tt0) REVERT: A 1112 MET cc_start: 0.7157 (mmm) cc_final: 0.6854 (mmm) REVERT: A 1147 TYR cc_start: 0.7789 (t80) cc_final: 0.7431 (t80) REVERT: A 1177 PRO cc_start: 0.8023 (Cg_endo) cc_final: 0.7493 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7350 (m-80) cc_final: 0.6572 (m-80) REVERT: A 1190 MET cc_start: 0.6962 (ttt) cc_final: 0.6374 (ttt) REVERT: L 75 ASP cc_start: 0.7438 (p0) cc_final: 0.6661 (m-30) REVERT: L 78 LEU cc_start: 0.7975 (tp) cc_final: 0.7692 (tp) REVERT: H 52 TRP cc_start: 0.6957 (OUTLIER) cc_final: 0.6269 (t-100) REVERT: H 103 LEU cc_start: 0.8987 (tp) cc_final: 0.8312 (tt) REVERT: B 78 MET cc_start: 0.7231 (mmm) cc_final: 0.7010 (tpp) REVERT: B 235 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7577 (mtmm) REVERT: B 259 LYS cc_start: 0.7689 (ptmt) cc_final: 0.7326 (ptmt) REVERT: B 328 ARG cc_start: 0.7086 (mpt180) cc_final: 0.6768 (mmt-90) REVERT: B 395 THR cc_start: 0.8113 (m) cc_final: 0.7882 (p) REVERT: B 478 VAL cc_start: 0.8447 (p) cc_final: 0.8196 (m) REVERT: B 596 ILE cc_start: 0.8692 (mm) cc_final: 0.8446 (mp) REVERT: B 626 ASP cc_start: 0.7086 (t0) cc_final: 0.6553 (t0) REVERT: B 689 SER cc_start: 0.7597 (t) cc_final: 0.7351 (t) REVERT: B 772 GLU cc_start: 0.7071 (tp30) cc_final: 0.6840 (tp30) REVERT: B 923 PHE cc_start: 0.7465 (m-80) cc_final: 0.7250 (m-80) REVERT: B 951 LEU cc_start: 0.8489 (mm) cc_final: 0.8196 (mt) REVERT: B 958 ASN cc_start: 0.7592 (m110) cc_final: 0.7242 (m-40) REVERT: B 1000 ASP cc_start: 0.7537 (t0) cc_final: 0.7304 (t70) REVERT: B 1048 LEU cc_start: 0.7885 (tp) cc_final: 0.7643 (tp) REVERT: B 1076 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: B 1080 ASP cc_start: 0.5866 (t0) cc_final: 0.5581 (t0) REVERT: B 1112 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6424 (mpp) REVERT: B 1139 VAL cc_start: 0.8381 (t) cc_final: 0.8024 (p) REVERT: B 1182 PHE cc_start: 0.7449 (m-80) cc_final: 0.7157 (m-80) REVERT: B 1189 TRP cc_start: 0.8463 (m100) cc_final: 0.8149 (m100) REVERT: B 1190 MET cc_start: 0.7021 (ttm) cc_final: 0.6619 (ttt) REVERT: D 75 ASP cc_start: 0.7459 (p0) cc_final: 0.7072 (m-30) REVERT: G 52 TRP cc_start: 0.6786 (OUTLIER) cc_final: 0.5815 (t-100) REVERT: G 102 TRP cc_start: 0.7730 (p-90) cc_final: 0.7280 (p-90) REVERT: G 103 LEU cc_start: 0.9001 (tp) cc_final: 0.8597 (tp) REVERT: C 180 LEU cc_start: 0.8632 (mt) cc_final: 0.8271 (mp) REVERT: C 235 LYS cc_start: 0.7777 (mtmm) cc_final: 0.7477 (mtmm) REVERT: C 241 TYR cc_start: 0.6943 (t80) cc_final: 0.6639 (t80) REVERT: C 259 LYS cc_start: 0.7626 (ptmt) cc_final: 0.7337 (ptmt) REVERT: C 325 VAL cc_start: 0.7620 (p) cc_final: 0.7403 (m) REVERT: C 326 TYR cc_start: 0.7266 (t80) cc_final: 0.6899 (t80) REVERT: C 342 ASN cc_start: 0.8088 (t0) cc_final: 0.7703 (t0) REVERT: C 478 VAL cc_start: 0.8316 (p) cc_final: 0.8076 (m) REVERT: C 544 LYS cc_start: 0.6581 (mmmt) cc_final: 0.6303 (mmmm) REVERT: C 680 VAL cc_start: 0.8437 (t) cc_final: 0.8220 (m) REVERT: C 699 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7611 (mtmm) REVERT: C 832 GLN cc_start: 0.7894 (mm110) cc_final: 0.7247 (mp10) REVERT: C 874 LYS cc_start: 0.6496 (mtmm) cc_final: 0.6233 (mtmm) REVERT: C 948 ILE cc_start: 0.8226 (mp) cc_final: 0.7885 (mm) REVERT: C 986 LEU cc_start: 0.7770 (mt) cc_final: 0.7466 (mt) REVERT: C 1005 ASN cc_start: 0.7427 (t0) cc_final: 0.7098 (t0) REVERT: C 1033 LYS cc_start: 0.8434 (tppt) cc_final: 0.8201 (ttmm) REVERT: C 1039 ASN cc_start: 0.7699 (t0) cc_final: 0.7446 (t0) REVERT: C 1177 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7473 (Cg_exo) REVERT: C 1182 PHE cc_start: 0.7300 (m-80) cc_final: 0.6556 (m-80) REVERT: C 1190 MET cc_start: 0.6771 (ttt) cc_final: 0.6429 (ttt) REVERT: E 42 LEU cc_start: 0.6391 (mt) cc_final: 0.6145 (mt) REVERT: E 54 TYR cc_start: 0.7422 (p90) cc_final: 0.7186 (p90) REVERT: E 84 GLU cc_start: 0.6702 (pp20) cc_final: 0.6150 (pp20) REVERT: I 103 LEU cc_start: 0.8945 (tp) cc_final: 0.8363 (tt) outliers start: 102 outliers final: 57 residues processed: 908 average time/residue: 0.4246 time to fit residues: 632.3261 Evaluate side-chains 907 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 843 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 730 TYR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 0.4980 chunk 230 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 302 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 364 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 697 ASN A1150 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN H 13 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B 860 GLN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS D 50 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN I 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34296 Z= 0.231 Angle : 0.603 9.179 46677 Z= 0.313 Chirality : 0.046 0.342 5376 Planarity : 0.004 0.043 5952 Dihedral : 6.470 96.940 5592 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.06 % Allowed : 16.67 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4176 helix: 0.22 (0.19), residues: 750 sheet: -0.55 (0.16), residues: 1044 loop : -1.13 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 102 HIS 0.006 0.001 HIS B 215 PHE 0.028 0.001 PHE B 122 TYR 0.024 0.002 TYR C 435 ARG 0.007 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 868 time to evaluate : 3.278 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: A 315 ASN cc_start: 0.7370 (p0) cc_final: 0.7127 (p0) REVERT: A 342 ASN cc_start: 0.7831 (t0) cc_final: 0.7153 (t0) REVERT: A 375 SER cc_start: 0.7695 (t) cc_final: 0.7311 (m) REVERT: A 425 ASP cc_start: 0.7307 (t70) cc_final: 0.7026 (t0) REVERT: A 437 LEU cc_start: 0.7920 (mt) cc_final: 0.7604 (mt) REVERT: A 478 VAL cc_start: 0.8413 (p) cc_final: 0.8197 (m) REVERT: A 596 ILE cc_start: 0.8670 (mm) cc_final: 0.8386 (mt) REVERT: A 731 ASN cc_start: 0.7553 (t0) cc_final: 0.7078 (t0) REVERT: A 1000 ASP cc_start: 0.7405 (t0) cc_final: 0.7171 (t0) REVERT: A 1076 GLU cc_start: 0.6633 (tt0) cc_final: 0.6065 (tt0) REVERT: A 1147 TYR cc_start: 0.7775 (t80) cc_final: 0.7472 (t80) REVERT: A 1177 PRO cc_start: 0.8079 (Cg_endo) cc_final: 0.7550 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7386 (m-80) cc_final: 0.6575 (m-80) REVERT: A 1190 MET cc_start: 0.7001 (ttt) cc_final: 0.6433 (ttt) REVERT: L 78 LEU cc_start: 0.7932 (tp) cc_final: 0.7706 (tp) REVERT: H 52 TRP cc_start: 0.6934 (OUTLIER) cc_final: 0.6193 (t-100) REVERT: H 103 LEU cc_start: 0.8916 (tp) cc_final: 0.8196 (tt) REVERT: B 29 LYS cc_start: 0.7590 (tptt) cc_final: 0.7218 (tppt) REVERT: B 235 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7523 (mtmm) REVERT: B 259 LYS cc_start: 0.7674 (ptmt) cc_final: 0.7312 (ptmt) REVERT: B 328 ARG cc_start: 0.7019 (mpt180) cc_final: 0.6483 (mpt180) REVERT: B 395 THR cc_start: 0.8017 (m) cc_final: 0.7777 (p) REVERT: B 478 VAL cc_start: 0.8437 (p) cc_final: 0.8213 (m) REVERT: B 617 ILE cc_start: 0.8109 (mp) cc_final: 0.7712 (mm) REVERT: B 626 ASP cc_start: 0.7045 (t0) cc_final: 0.6529 (t0) REVERT: B 638 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6255 (mm-30) REVERT: B 772 GLU cc_start: 0.7238 (tp30) cc_final: 0.6885 (tp30) REVERT: B 923 PHE cc_start: 0.7455 (m-80) cc_final: 0.7230 (m-80) REVERT: B 951 LEU cc_start: 0.8495 (mm) cc_final: 0.8217 (mt) REVERT: B 958 ASN cc_start: 0.7617 (m110) cc_final: 0.7246 (m-40) REVERT: B 1000 ASP cc_start: 0.7342 (t0) cc_final: 0.6983 (t0) REVERT: B 1048 LEU cc_start: 0.7871 (tp) cc_final: 0.7607 (tp) REVERT: B 1112 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6470 (mpp) REVERT: B 1139 VAL cc_start: 0.8329 (t) cc_final: 0.7959 (p) REVERT: B 1182 PHE cc_start: 0.7493 (m-80) cc_final: 0.7115 (m-80) REVERT: B 1189 TRP cc_start: 0.8466 (m100) cc_final: 0.8150 (m100) REVERT: B 1190 MET cc_start: 0.7043 (ttm) cc_final: 0.6636 (ttt) REVERT: D 4 MET cc_start: 0.4536 (mpp) cc_final: 0.4327 (mpp) REVERT: G 52 TRP cc_start: 0.6789 (OUTLIER) cc_final: 0.5868 (t-100) REVERT: G 103 LEU cc_start: 0.8952 (tp) cc_final: 0.8547 (tp) REVERT: C 180 LEU cc_start: 0.8686 (mt) cc_final: 0.8332 (mp) REVERT: C 235 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7471 (mtmm) REVERT: C 259 LYS cc_start: 0.7624 (ptmt) cc_final: 0.7330 (ptmt) REVERT: C 325 VAL cc_start: 0.7618 (p) cc_final: 0.7415 (m) REVERT: C 328 ARG cc_start: 0.6919 (mpt180) cc_final: 0.6585 (mpt180) REVERT: C 329 LYS cc_start: 0.7980 (mttt) cc_final: 0.7469 (ttmm) REVERT: C 342 ASN cc_start: 0.8099 (t0) cc_final: 0.7700 (t0) REVERT: C 680 VAL cc_start: 0.8505 (t) cc_final: 0.8254 (m) REVERT: C 699 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7706 (mtmm) REVERT: C 832 GLN cc_start: 0.7882 (mm110) cc_final: 0.7278 (mp10) REVERT: C 874 LYS cc_start: 0.6505 (mtmm) cc_final: 0.6292 (mtmm) REVERT: C 1005 ASN cc_start: 0.7468 (t0) cc_final: 0.7115 (t0) REVERT: C 1033 LYS cc_start: 0.8420 (tppt) cc_final: 0.8153 (ttmm) REVERT: C 1039 ASN cc_start: 0.7703 (t0) cc_final: 0.7487 (t0) REVERT: C 1182 PHE cc_start: 0.7307 (m-80) cc_final: 0.6985 (m-80) REVERT: C 1190 MET cc_start: 0.6726 (ttt) cc_final: 0.6289 (ttt) REVERT: E 42 LEU cc_start: 0.6359 (mt) cc_final: 0.6107 (mt) REVERT: E 54 TYR cc_start: 0.7453 (p90) cc_final: 0.7225 (p90) REVERT: E 84 GLU cc_start: 0.6733 (pp20) cc_final: 0.6287 (pp20) outliers start: 112 outliers final: 76 residues processed: 912 average time/residue: 0.4275 time to fit residues: 639.0802 Evaluate side-chains 917 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 838 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 730 TYR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 7.9990 chunk 365 optimal weight: 0.0570 chunk 80 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 406 optimal weight: 1.9990 chunk 337 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 697 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 844 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34296 Z= 0.212 Angle : 0.601 11.082 46677 Z= 0.310 Chirality : 0.046 0.337 5376 Planarity : 0.004 0.052 5952 Dihedral : 6.204 94.918 5592 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.11 % Allowed : 18.14 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4176 helix: 0.40 (0.19), residues: 729 sheet: -0.63 (0.16), residues: 1071 loop : -1.09 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 102 HIS 0.006 0.001 HIS L 31 PHE 0.026 0.001 PHE B 203 TYR 0.024 0.001 TYR C 435 ARG 0.008 0.000 ARG C 991 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 864 time to evaluate : 3.824 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5870 (tt) REVERT: A 136 TYR cc_start: 0.8225 (m-80) cc_final: 0.7726 (m-10) REVERT: A 315 ASN cc_start: 0.7438 (p0) cc_final: 0.7064 (p0) REVERT: A 328 ARG cc_start: 0.6891 (mpt180) cc_final: 0.6583 (mmt180) REVERT: A 335 CYS cc_start: 0.5020 (m) cc_final: 0.4662 (m) REVERT: A 342 ASN cc_start: 0.7844 (t0) cc_final: 0.7145 (t0) REVERT: A 375 SER cc_start: 0.7677 (t) cc_final: 0.7290 (m) REVERT: A 425 ASP cc_start: 0.7237 (t70) cc_final: 0.6915 (t0) REVERT: A 437 LEU cc_start: 0.7891 (mt) cc_final: 0.7536 (mt) REVERT: A 478 VAL cc_start: 0.8382 (p) cc_final: 0.8176 (m) REVERT: A 596 ILE cc_start: 0.8636 (mm) cc_final: 0.8381 (mt) REVERT: A 626 ASP cc_start: 0.6694 (t0) cc_final: 0.6296 (t0) REVERT: A 694 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6976 (tp) REVERT: A 731 ASN cc_start: 0.7530 (t0) cc_final: 0.7042 (t0) REVERT: A 860 GLN cc_start: 0.6937 (mp10) cc_final: 0.6725 (mp10) REVERT: A 976 TRP cc_start: 0.6723 (m-90) cc_final: 0.6125 (m-90) REVERT: A 1062 SER cc_start: 0.6691 (OUTLIER) cc_final: 0.6461 (p) REVERT: A 1073 LEU cc_start: 0.7353 (pt) cc_final: 0.7119 (pp) REVERT: A 1147 TYR cc_start: 0.7767 (t80) cc_final: 0.7462 (t80) REVERT: A 1177 PRO cc_start: 0.8098 (Cg_endo) cc_final: 0.7465 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7385 (m-80) cc_final: 0.6558 (m-80) REVERT: A 1190 MET cc_start: 0.7057 (ttt) cc_final: 0.6665 (ttt) REVERT: L 78 LEU cc_start: 0.7899 (tp) cc_final: 0.7671 (tp) REVERT: H 52 TRP cc_start: 0.6884 (OUTLIER) cc_final: 0.6213 (t-100) REVERT: H 58 LYS cc_start: 0.8227 (mttt) cc_final: 0.7859 (mptt) REVERT: H 103 LEU cc_start: 0.8890 (tp) cc_final: 0.8379 (tp) REVERT: B 235 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7526 (mtmm) REVERT: B 259 LYS cc_start: 0.7669 (ptmt) cc_final: 0.7313 (ptmt) REVERT: B 325 VAL cc_start: 0.7635 (p) cc_final: 0.7394 (m) REVERT: B 328 ARG cc_start: 0.7034 (mpt180) cc_final: 0.6516 (mpt180) REVERT: B 395 THR cc_start: 0.8029 (m) cc_final: 0.7807 (p) REVERT: B 478 VAL cc_start: 0.8443 (p) cc_final: 0.8210 (m) REVERT: B 596 ILE cc_start: 0.8636 (mm) cc_final: 0.8393 (mp) REVERT: B 610 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8276 (pp) REVERT: B 626 ASP cc_start: 0.7019 (t0) cc_final: 0.6304 (t0) REVERT: B 638 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6391 (mm-30) REVERT: B 711 ARG cc_start: 0.7279 (mtm180) cc_final: 0.6876 (mtm180) REVERT: B 772 GLU cc_start: 0.7116 (tp30) cc_final: 0.6754 (tp30) REVERT: B 798 PHE cc_start: 0.7852 (p90) cc_final: 0.7588 (p90) REVERT: B 923 PHE cc_start: 0.7368 (m-80) cc_final: 0.7143 (m-80) REVERT: B 951 LEU cc_start: 0.8492 (mm) cc_final: 0.8218 (mt) REVERT: B 958 ASN cc_start: 0.7581 (m110) cc_final: 0.7208 (m-40) REVERT: B 1000 ASP cc_start: 0.7253 (t0) cc_final: 0.7018 (t0) REVERT: B 1048 LEU cc_start: 0.7861 (tp) cc_final: 0.7592 (tp) REVERT: B 1112 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6467 (mpp) REVERT: B 1139 VAL cc_start: 0.8345 (t) cc_final: 0.7995 (p) REVERT: B 1181 TYR cc_start: 0.7748 (m-80) cc_final: 0.7429 (m-10) REVERT: B 1182 PHE cc_start: 0.7489 (m-80) cc_final: 0.7190 (m-80) REVERT: B 1189 TRP cc_start: 0.8458 (m100) cc_final: 0.8182 (m100) REVERT: B 1190 MET cc_start: 0.7040 (ttm) cc_final: 0.6611 (ttt) REVERT: B 1198 TYR cc_start: 0.7243 (t80) cc_final: 0.6963 (t80) REVERT: G 52 TRP cc_start: 0.6748 (OUTLIER) cc_final: 0.5842 (t-100) REVERT: G 102 TRP cc_start: 0.7770 (p-90) cc_final: 0.7349 (p-90) REVERT: G 103 LEU cc_start: 0.8935 (tp) cc_final: 0.8520 (tp) REVERT: C 180 LEU cc_start: 0.8670 (mt) cc_final: 0.8356 (mp) REVERT: C 235 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7419 (mtmm) REVERT: C 259 LYS cc_start: 0.7617 (ptmt) cc_final: 0.7370 (ptmt) REVERT: C 328 ARG cc_start: 0.6875 (mpt180) cc_final: 0.6666 (mpt180) REVERT: C 329 LYS cc_start: 0.8001 (mttt) cc_final: 0.7738 (mttt) REVERT: C 342 ASN cc_start: 0.8072 (t0) cc_final: 0.7702 (t0) REVERT: C 832 GLN cc_start: 0.7862 (mm110) cc_final: 0.7285 (mp10) REVERT: C 874 LYS cc_start: 0.6496 (mtmm) cc_final: 0.6283 (mtmm) REVERT: C 1005 ASN cc_start: 0.7494 (t0) cc_final: 0.7145 (t0) REVERT: C 1033 LYS cc_start: 0.8409 (tppt) cc_final: 0.8128 (ttmm) REVERT: C 1039 ASN cc_start: 0.7695 (t0) cc_final: 0.7457 (t0) REVERT: C 1073 LEU cc_start: 0.7006 (pt) cc_final: 0.6754 (pt) REVERT: C 1182 PHE cc_start: 0.7288 (m-80) cc_final: 0.6958 (m-80) REVERT: C 1190 MET cc_start: 0.6722 (ttt) cc_final: 0.6334 (ttt) REVERT: E 42 LEU cc_start: 0.6502 (mt) cc_final: 0.6225 (mt) REVERT: E 84 GLU cc_start: 0.6735 (pp20) cc_final: 0.6299 (pp20) outliers start: 114 outliers final: 80 residues processed: 914 average time/residue: 0.4226 time to fit residues: 636.7376 Evaluate side-chains 929 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 842 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 730 TYR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 229 optimal weight: 0.1980 chunk 342 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 404 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 697 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN B1084 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 410 GLN C 585 GLN C 844 ASN C 858 GLN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 34296 Z= 0.264 Angle : 0.627 9.809 46677 Z= 0.325 Chirality : 0.047 0.340 5376 Planarity : 0.004 0.045 5952 Dihedral : 6.137 92.636 5592 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.28 % Allowed : 18.72 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4176 helix: 0.40 (0.19), residues: 726 sheet: -0.58 (0.16), residues: 1050 loop : -1.13 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 102 HIS 0.006 0.001 HIS B 215 PHE 0.045 0.002 PHE C 122 TYR 0.026 0.002 TYR C 435 ARG 0.007 0.000 ARG C 991 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 858 time to evaluate : 3.123 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: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8203 (tptt) cc_final: 0.7719 (tppt) REVERT: A 125 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5951 (tt) REVERT: A 136 TYR cc_start: 0.8243 (m-80) cc_final: 0.7781 (m-10) REVERT: A 315 ASN cc_start: 0.7441 (p0) cc_final: 0.7094 (p0) REVERT: A 328 ARG cc_start: 0.6934 (mpt180) cc_final: 0.6529 (mmt180) REVERT: A 335 CYS cc_start: 0.5041 (m) cc_final: 0.4698 (m) REVERT: A 342 ASN cc_start: 0.7863 (t0) cc_final: 0.7187 (t0) REVERT: A 375 SER cc_start: 0.7682 (t) cc_final: 0.7319 (m) REVERT: A 425 ASP cc_start: 0.7265 (t70) cc_final: 0.6922 (t0) REVERT: A 437 LEU cc_start: 0.7963 (mt) cc_final: 0.7593 (mt) REVERT: A 596 ILE cc_start: 0.8605 (mm) cc_final: 0.8398 (mt) REVERT: A 626 ASP cc_start: 0.6698 (t0) cc_final: 0.6195 (t0) REVERT: A 694 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6985 (tp) REVERT: A 731 ASN cc_start: 0.7606 (t0) cc_final: 0.7102 (t0) REVERT: A 976 TRP cc_start: 0.6764 (m-90) cc_final: 0.6118 (m-90) REVERT: A 1147 TYR cc_start: 0.7787 (t80) cc_final: 0.7564 (t80) REVERT: A 1177 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7544 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7428 (m-80) cc_final: 0.6573 (m-80) REVERT: A 1190 MET cc_start: 0.7090 (ttt) cc_final: 0.6587 (ttt) REVERT: A 1198 TYR cc_start: 0.7395 (t80) cc_final: 0.6831 (t80) REVERT: H 52 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6312 (t-100) REVERT: H 58 LYS cc_start: 0.8261 (mttt) cc_final: 0.8001 (mptt) REVERT: H 103 LEU cc_start: 0.8870 (tp) cc_final: 0.8420 (tp) REVERT: B 29 LYS cc_start: 0.7555 (tptt) cc_final: 0.7176 (tppt) REVERT: B 168 MET cc_start: 0.5595 (mmm) cc_final: 0.4908 (mmm) REVERT: B 235 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7534 (mtmm) REVERT: B 259 LYS cc_start: 0.7648 (ptmt) cc_final: 0.7296 (ptmt) REVERT: B 325 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7425 (m) REVERT: B 328 ARG cc_start: 0.7041 (mpt180) cc_final: 0.6518 (mpt180) REVERT: B 395 THR cc_start: 0.8012 (m) cc_final: 0.7808 (p) REVERT: B 478 VAL cc_start: 0.8477 (p) cc_final: 0.8238 (m) REVERT: B 544 LYS cc_start: 0.6228 (mmmm) cc_final: 0.5907 (mmtp) REVERT: B 596 ILE cc_start: 0.8604 (mm) cc_final: 0.8399 (mp) REVERT: B 617 ILE cc_start: 0.7883 (mp) cc_final: 0.7519 (mm) REVERT: B 626 ASP cc_start: 0.7031 (t0) cc_final: 0.6339 (t0) REVERT: B 638 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6464 (mm-30) REVERT: B 711 ARG cc_start: 0.7363 (mtm180) cc_final: 0.6999 (mtm180) REVERT: B 719 PHE cc_start: 0.7881 (p90) cc_final: 0.7365 (p90) REVERT: B 798 PHE cc_start: 0.7900 (p90) cc_final: 0.7666 (p90) REVERT: B 860 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7185 (mt0) REVERT: B 913 PHE cc_start: 0.6971 (m-80) cc_final: 0.6473 (m-80) REVERT: B 951 LEU cc_start: 0.8493 (mm) cc_final: 0.8218 (mt) REVERT: B 958 ASN cc_start: 0.7601 (m110) cc_final: 0.7247 (m-40) REVERT: B 1000 ASP cc_start: 0.7201 (t0) cc_final: 0.6770 (t0) REVERT: B 1048 LEU cc_start: 0.7904 (tp) cc_final: 0.7611 (tp) REVERT: B 1112 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6609 (mpp) REVERT: B 1139 VAL cc_start: 0.8382 (t) cc_final: 0.8007 (p) REVERT: B 1147 TYR cc_start: 0.7704 (t80) cc_final: 0.7380 (t80) REVERT: B 1181 TYR cc_start: 0.7782 (m-80) cc_final: 0.7394 (m-10) REVERT: B 1182 PHE cc_start: 0.7534 (m-80) cc_final: 0.7145 (m-80) REVERT: B 1189 TRP cc_start: 0.8472 (m100) cc_final: 0.8205 (m100) REVERT: B 1190 MET cc_start: 0.7030 (ttm) cc_final: 0.6624 (ttt) REVERT: B 1198 TYR cc_start: 0.7279 (t80) cc_final: 0.6404 (t80) REVERT: G 52 TRP cc_start: 0.6792 (OUTLIER) cc_final: 0.5884 (t-100) REVERT: G 103 LEU cc_start: 0.8889 (tp) cc_final: 0.8462 (tp) REVERT: C 180 LEU cc_start: 0.8710 (mt) cc_final: 0.8363 (mp) REVERT: C 235 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7383 (mtmm) REVERT: C 259 LYS cc_start: 0.7637 (ptmt) cc_final: 0.7393 (ptmt) REVERT: C 328 ARG cc_start: 0.6905 (mpt180) cc_final: 0.6587 (mpt180) REVERT: C 329 LYS cc_start: 0.8023 (mttt) cc_final: 0.7473 (ttmm) REVERT: C 342 ASN cc_start: 0.8140 (t0) cc_final: 0.7776 (t0) REVERT: C 675 CYS cc_start: 0.4696 (OUTLIER) cc_final: 0.4326 (p) REVERT: C 832 GLN cc_start: 0.7912 (mm110) cc_final: 0.7323 (mp10) REVERT: C 858 GLN cc_start: 0.6369 (mm-40) cc_final: 0.6099 (mm-40) REVERT: C 976 TRP cc_start: 0.6992 (m-90) cc_final: 0.6778 (m-90) REVERT: C 1033 LYS cc_start: 0.8416 (tppt) cc_final: 0.8150 (ttmm) REVERT: C 1182 PHE cc_start: 0.7342 (m-80) cc_final: 0.6987 (m-80) REVERT: C 1190 MET cc_start: 0.6782 (ttt) cc_final: 0.6360 (ttt) REVERT: E 42 LEU cc_start: 0.6390 (mt) cc_final: 0.6140 (mt) REVERT: E 84 GLU cc_start: 0.6799 (pp20) cc_final: 0.6330 (pp20) REVERT: E 101 LEU cc_start: 0.8228 (mp) cc_final: 0.8016 (mp) outliers start: 120 outliers final: 86 residues processed: 914 average time/residue: 0.4170 time to fit residues: 631.2601 Evaluate side-chains 932 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 838 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 644 TYR Chi-restraints excluded: chain C residue 675 CYS Chi-restraints excluded: chain C residue 730 TYR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 318 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN B1084 ASN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN C 173 GLN C 248 HIS C 590 ASN C 844 ASN C1005 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34296 Z= 0.243 Angle : 0.636 12.527 46677 Z= 0.327 Chirality : 0.047 0.336 5376 Planarity : 0.004 0.050 5952 Dihedral : 5.978 90.277 5592 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.36 % Allowed : 19.37 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4176 helix: 0.27 (0.19), residues: 735 sheet: -0.63 (0.16), residues: 1035 loop : -1.12 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 102 HIS 0.005 0.001 HIS A 215 PHE 0.044 0.002 PHE C 122 TYR 0.025 0.002 TYR C 435 ARG 0.008 0.000 ARG C 991 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 857 time to evaluate : 3.593 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8171 (tptt) cc_final: 0.7767 (tppt) REVERT: A 125 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.6061 (tp) REVERT: A 136 TYR cc_start: 0.8262 (m-80) cc_final: 0.7789 (m-10) REVERT: A 315 ASN cc_start: 0.7393 (p0) cc_final: 0.7071 (p0) REVERT: A 328 ARG cc_start: 0.6826 (mpt180) cc_final: 0.6535 (mmt-90) REVERT: A 335 CYS cc_start: 0.5036 (m) cc_final: 0.4686 (m) REVERT: A 342 ASN cc_start: 0.7848 (t0) cc_final: 0.7160 (t0) REVERT: A 375 SER cc_start: 0.7689 (t) cc_final: 0.7313 (m) REVERT: A 425 ASP cc_start: 0.7264 (t70) cc_final: 0.6927 (t0) REVERT: A 437 LEU cc_start: 0.7976 (mt) cc_final: 0.7627 (mt) REVERT: A 626 ASP cc_start: 0.6626 (t0) cc_final: 0.6253 (t0) REVERT: A 694 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6976 (tp) REVERT: A 731 ASN cc_start: 0.7603 (t0) cc_final: 0.7095 (t0) REVERT: A 774 PHE cc_start: 0.6930 (m-80) cc_final: 0.6730 (m-10) REVERT: A 858 GLN cc_start: 0.6661 (mm-40) cc_final: 0.6411 (mm-40) REVERT: A 976 TRP cc_start: 0.6798 (m-90) cc_final: 0.6144 (m-90) REVERT: A 1147 TYR cc_start: 0.7786 (t80) cc_final: 0.7473 (t80) REVERT: A 1177 PRO cc_start: 0.8153 (Cg_endo) cc_final: 0.7538 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7405 (m-80) cc_final: 0.6579 (m-80) REVERT: A 1190 MET cc_start: 0.7068 (ttt) cc_final: 0.6648 (ttt) REVERT: A 1198 TYR cc_start: 0.7361 (t80) cc_final: 0.6823 (t80) REVERT: L 79 LYS cc_start: 0.7881 (tttt) cc_final: 0.7626 (tptt) REVERT: H 52 TRP cc_start: 0.6943 (OUTLIER) cc_final: 0.6196 (t-100) REVERT: H 58 LYS cc_start: 0.8248 (mttt) cc_final: 0.7959 (mptt) REVERT: H 103 LEU cc_start: 0.8895 (tp) cc_final: 0.8586 (tp) REVERT: B 29 LYS cc_start: 0.7606 (tptt) cc_final: 0.7324 (tptt) REVERT: B 136 TYR cc_start: 0.8313 (m-80) cc_final: 0.8058 (m-80) REVERT: B 168 MET cc_start: 0.5628 (mmm) cc_final: 0.4941 (mmm) REVERT: B 235 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7499 (mtmm) REVERT: B 259 LYS cc_start: 0.7656 (ptmt) cc_final: 0.7296 (ptmt) REVERT: B 325 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7443 (m) REVERT: B 328 ARG cc_start: 0.6947 (mpt180) cc_final: 0.6671 (mmt180) REVERT: B 395 THR cc_start: 0.8018 (m) cc_final: 0.7782 (p) REVERT: B 478 VAL cc_start: 0.8469 (p) cc_final: 0.8233 (m) REVERT: B 544 LYS cc_start: 0.6202 (mmmm) cc_final: 0.5790 (mmtp) REVERT: B 596 ILE cc_start: 0.8595 (mm) cc_final: 0.8388 (mp) REVERT: B 626 ASP cc_start: 0.7026 (t0) cc_final: 0.6465 (t0) REVERT: B 638 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6418 (mm-30) REVERT: B 711 ARG cc_start: 0.7347 (mtm180) cc_final: 0.7046 (mtm180) REVERT: B 719 PHE cc_start: 0.7895 (p90) cc_final: 0.7392 (p90) REVERT: B 798 PHE cc_start: 0.7884 (p90) cc_final: 0.7669 (p90) REVERT: B 860 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: B 923 PHE cc_start: 0.7350 (m-80) cc_final: 0.7146 (m-80) REVERT: B 951 LEU cc_start: 0.8505 (mm) cc_final: 0.8233 (mt) REVERT: B 958 ASN cc_start: 0.7594 (m110) cc_final: 0.7201 (m-40) REVERT: B 986 LEU cc_start: 0.8024 (mt) cc_final: 0.7722 (mt) REVERT: B 1000 ASP cc_start: 0.7230 (t0) cc_final: 0.6764 (t0) REVERT: B 1033 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8364 (ttmm) REVERT: B 1048 LEU cc_start: 0.7859 (tp) cc_final: 0.7586 (tp) REVERT: B 1112 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6669 (mpp) REVERT: B 1139 VAL cc_start: 0.8353 (t) cc_final: 0.7985 (p) REVERT: B 1147 TYR cc_start: 0.7660 (t80) cc_final: 0.7326 (t80) REVERT: B 1181 TYR cc_start: 0.7813 (m-80) cc_final: 0.7420 (m-10) REVERT: B 1182 PHE cc_start: 0.7481 (m-80) cc_final: 0.7172 (m-80) REVERT: B 1189 TRP cc_start: 0.8486 (m100) cc_final: 0.8224 (m100) REVERT: B 1190 MET cc_start: 0.7062 (ttm) cc_final: 0.6584 (ttt) REVERT: B 1198 TYR cc_start: 0.7294 (t80) cc_final: 0.6483 (t80) REVERT: G 52 TRP cc_start: 0.6776 (OUTLIER) cc_final: 0.6008 (t-100) REVERT: G 103 LEU cc_start: 0.8904 (tp) cc_final: 0.8473 (tp) REVERT: C 180 LEU cc_start: 0.8715 (mt) cc_final: 0.8370 (mp) REVERT: C 235 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7375 (mtmm) REVERT: C 259 LYS cc_start: 0.7637 (ptmt) cc_final: 0.7395 (ptmt) REVERT: C 328 ARG cc_start: 0.6891 (mpt180) cc_final: 0.6526 (mpt180) REVERT: C 329 LYS cc_start: 0.7995 (mttt) cc_final: 0.7465 (ttmm) REVERT: C 342 ASN cc_start: 0.8134 (t0) cc_final: 0.7753 (t0) REVERT: C 832 GLN cc_start: 0.7912 (mm110) cc_final: 0.7323 (mp10) REVERT: C 976 TRP cc_start: 0.7021 (m-90) cc_final: 0.6785 (m-90) REVERT: C 1005 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7159 (t0) REVERT: C 1033 LYS cc_start: 0.8395 (tppt) cc_final: 0.8175 (ttmm) REVERT: C 1182 PHE cc_start: 0.7315 (m-80) cc_final: 0.6960 (m-80) REVERT: C 1190 MET cc_start: 0.6785 (ttt) cc_final: 0.6349 (ttt) REVERT: C 1205 ASN cc_start: 0.8363 (m110) cc_final: 0.8158 (m110) REVERT: E 42 LEU cc_start: 0.6323 (mt) cc_final: 0.6087 (mt) REVERT: E 84 GLU cc_start: 0.6704 (pp20) cc_final: 0.6214 (pp20) REVERT: I 83 MET cc_start: 0.6807 (pmm) cc_final: 0.6333 (pmm) outliers start: 123 outliers final: 87 residues processed: 914 average time/residue: 0.4211 time to fit residues: 633.3725 Evaluate side-chains 942 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 847 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 644 TYR Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1137 SER Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 4.9990 chunk 387 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 296 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 356 optimal weight: 0.8980 chunk 375 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 GLN B1084 ASN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 844 ASN C1005 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34296 Z= 0.217 Angle : 0.640 11.509 46677 Z= 0.329 Chirality : 0.047 0.332 5376 Planarity : 0.004 0.051 5952 Dihedral : 5.838 88.198 5592 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.90 % Allowed : 20.25 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4176 helix: 0.23 (0.19), residues: 741 sheet: -0.61 (0.16), residues: 1017 loop : -1.09 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 102 HIS 0.014 0.001 HIS L 31 PHE 0.044 0.002 PHE A 771 TYR 0.040 0.002 TYR B 68 ARG 0.008 0.000 ARG C 991 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 853 time to evaluate : 3.459 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: symmetry clash REVERT: A 29 LYS cc_start: 0.8151 (tptt) cc_final: 0.7742 (tppt) REVERT: A 136 TYR cc_start: 0.8257 (m-80) cc_final: 0.7785 (m-10) REVERT: A 315 ASN cc_start: 0.7400 (p0) cc_final: 0.7012 (p0) REVERT: A 328 ARG cc_start: 0.6749 (mpt180) cc_final: 0.6516 (mmt-90) REVERT: A 335 CYS cc_start: 0.5022 (m) cc_final: 0.4677 (m) REVERT: A 342 ASN cc_start: 0.7826 (t0) cc_final: 0.7155 (t0) REVERT: A 375 SER cc_start: 0.7656 (t) cc_final: 0.7295 (m) REVERT: A 425 ASP cc_start: 0.7271 (t70) cc_final: 0.6935 (t0) REVERT: A 437 LEU cc_start: 0.7966 (mt) cc_final: 0.7557 (mt) REVERT: A 573 GLN cc_start: 0.7650 (mp10) cc_final: 0.7435 (mp10) REVERT: A 626 ASP cc_start: 0.6654 (t0) cc_final: 0.6233 (t0) REVERT: A 694 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6960 (tp) REVERT: A 731 ASN cc_start: 0.7568 (t0) cc_final: 0.7072 (t0) REVERT: A 772 GLU cc_start: 0.7346 (tp30) cc_final: 0.6983 (tp30) REVERT: A 858 GLN cc_start: 0.6644 (mm-40) cc_final: 0.6401 (mm-40) REVERT: A 937 ARG cc_start: 0.7095 (mmm-85) cc_final: 0.6696 (mmm-85) REVERT: A 976 TRP cc_start: 0.6783 (m-90) cc_final: 0.6140 (m-90) REVERT: A 1147 TYR cc_start: 0.7798 (t80) cc_final: 0.7522 (t80) REVERT: A 1177 PRO cc_start: 0.8149 (Cg_endo) cc_final: 0.7514 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7391 (m-80) cc_final: 0.6543 (m-80) REVERT: A 1190 MET cc_start: 0.7103 (ttt) cc_final: 0.6700 (ttt) REVERT: A 1198 TYR cc_start: 0.7361 (t80) cc_final: 0.6821 (t80) REVERT: L 79 LYS cc_start: 0.7974 (tttt) cc_final: 0.7697 (tptt) REVERT: H 52 TRP cc_start: 0.6933 (OUTLIER) cc_final: 0.6300 (t-100) REVERT: H 58 LYS cc_start: 0.8229 (mttt) cc_final: 0.7934 (mptt) REVERT: H 103 LEU cc_start: 0.8879 (tp) cc_final: 0.8589 (tp) REVERT: B 29 LYS cc_start: 0.7599 (tptt) cc_final: 0.7312 (tptt) REVERT: B 136 TYR cc_start: 0.8280 (m-80) cc_final: 0.8056 (m-80) REVERT: B 168 MET cc_start: 0.5666 (mmm) cc_final: 0.4945 (mmm) REVERT: B 235 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7474 (mtmm) REVERT: B 259 LYS cc_start: 0.7680 (ptmt) cc_final: 0.7286 (ptmt) REVERT: B 328 ARG cc_start: 0.6903 (mpt180) cc_final: 0.6465 (mpt180) REVERT: B 395 THR cc_start: 0.8003 (m) cc_final: 0.7765 (p) REVERT: B 478 VAL cc_start: 0.8430 (p) cc_final: 0.8225 (m) REVERT: B 544 LYS cc_start: 0.6184 (mmmm) cc_final: 0.5784 (mmtp) REVERT: B 626 ASP cc_start: 0.7044 (t0) cc_final: 0.6346 (t0) REVERT: B 638 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 711 ARG cc_start: 0.7312 (mtm180) cc_final: 0.7067 (mtm180) REVERT: B 719 PHE cc_start: 0.7905 (p90) cc_final: 0.7414 (p90) REVERT: B 833 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 838 SER cc_start: 0.6730 (t) cc_final: 0.6445 (t) REVERT: B 860 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: B 913 PHE cc_start: 0.7086 (m-80) cc_final: 0.6854 (m-80) REVERT: B 951 LEU cc_start: 0.8479 (mm) cc_final: 0.8207 (mt) REVERT: B 986 LEU cc_start: 0.8018 (mt) cc_final: 0.7690 (mt) REVERT: B 1000 ASP cc_start: 0.7209 (t0) cc_final: 0.6813 (t0) REVERT: B 1033 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8370 (ttmm) REVERT: B 1048 LEU cc_start: 0.7844 (tp) cc_final: 0.7571 (tp) REVERT: B 1112 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6631 (mpp) REVERT: B 1139 VAL cc_start: 0.8318 (t) cc_final: 0.7962 (p) REVERT: B 1147 TYR cc_start: 0.7647 (t80) cc_final: 0.7338 (t80) REVERT: B 1181 TYR cc_start: 0.7796 (m-80) cc_final: 0.7403 (m-10) REVERT: B 1182 PHE cc_start: 0.7483 (m-80) cc_final: 0.7168 (m-80) REVERT: B 1189 TRP cc_start: 0.8487 (m100) cc_final: 0.8241 (m100) REVERT: B 1190 MET cc_start: 0.7025 (ttm) cc_final: 0.6574 (ttt) REVERT: B 1198 TYR cc_start: 0.7270 (t80) cc_final: 0.6466 (t80) REVERT: G 45 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7480 (mm) REVERT: G 52 TRP cc_start: 0.6770 (OUTLIER) cc_final: 0.6004 (t-100) REVERT: G 103 LEU cc_start: 0.8861 (tp) cc_final: 0.8467 (tp) REVERT: C 180 LEU cc_start: 0.8720 (mt) cc_final: 0.8389 (mp) REVERT: C 235 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7390 (mtmm) REVERT: C 259 LYS cc_start: 0.7644 (ptmt) cc_final: 0.7390 (ptmt) REVERT: C 328 ARG cc_start: 0.6982 (mpt180) cc_final: 0.6371 (mpt180) REVERT: C 329 LYS cc_start: 0.7980 (mttt) cc_final: 0.7537 (tttp) REVERT: C 342 ASN cc_start: 0.8120 (t0) cc_final: 0.7711 (t0) REVERT: C 626 ASP cc_start: 0.6432 (t0) cc_final: 0.5567 (t0) REVERT: C 631 LEU cc_start: 0.8593 (mm) cc_final: 0.8122 (mt) REVERT: C 832 GLN cc_start: 0.7893 (mm110) cc_final: 0.7306 (mp10) REVERT: C 976 TRP cc_start: 0.6985 (m-90) cc_final: 0.6738 (m-90) REVERT: C 1033 LYS cc_start: 0.8377 (tppt) cc_final: 0.8175 (ttmm) REVERT: C 1039 ASN cc_start: 0.7708 (t0) cc_final: 0.7471 (t0) REVERT: C 1182 PHE cc_start: 0.7298 (m-80) cc_final: 0.6962 (m-80) REVERT: C 1190 MET cc_start: 0.6907 (ttt) cc_final: 0.6538 (ttt) REVERT: E 42 LEU cc_start: 0.6317 (mt) cc_final: 0.6081 (mt) REVERT: E 84 GLU cc_start: 0.6656 (pp20) cc_final: 0.6233 (pp20) REVERT: I 83 MET cc_start: 0.6801 (pmm) cc_final: 0.6360 (pmm) outliers start: 106 outliers final: 82 residues processed: 901 average time/residue: 0.4273 time to fit residues: 633.9891 Evaluate side-chains 927 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 838 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 590 ASN Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1137 SER Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 3.9990 chunk 398 optimal weight: 30.0000 chunk 243 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 418 optimal weight: 4.9990 chunk 385 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 257 optimal weight: 0.0030 chunk 204 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 182 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B1150 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 403 ASN C 844 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.154 34296 Z= 0.490 Angle : 0.776 11.353 46677 Z= 0.409 Chirality : 0.052 0.359 5376 Planarity : 0.005 0.055 5952 Dihedral : 6.204 85.354 5592 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.76 % Allowed : 20.93 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 4176 helix: -0.36 (0.18), residues: 747 sheet: -0.85 (0.16), residues: 1086 loop : -1.36 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 40 HIS 0.011 0.002 HIS L 31 PHE 0.038 0.003 PHE A 771 TYR 0.053 0.003 TYR B 68 ARG 0.010 0.001 ARG C 991 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 899 time to evaluate : 3.363 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: A 136 TYR cc_start: 0.8247 (m-80) cc_final: 0.7792 (m-80) REVERT: A 315 ASN cc_start: 0.7518 (p0) cc_final: 0.7256 (p0) REVERT: A 328 ARG cc_start: 0.6726 (mpt180) cc_final: 0.6316 (mmt-90) REVERT: A 335 CYS cc_start: 0.5070 (m) cc_final: 0.4736 (m) REVERT: A 342 ASN cc_start: 0.7882 (t0) cc_final: 0.7216 (t0) REVERT: A 375 SER cc_start: 0.7769 (t) cc_final: 0.7382 (m) REVERT: A 425 ASP cc_start: 0.7354 (t70) cc_final: 0.7014 (t0) REVERT: A 437 LEU cc_start: 0.8123 (mt) cc_final: 0.7666 (mt) REVERT: A 626 ASP cc_start: 0.6615 (t0) cc_final: 0.6177 (t0) REVERT: A 679 ARG cc_start: 0.7246 (mtp85) cc_final: 0.7002 (ptm160) REVERT: A 694 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7045 (tp) REVERT: A 731 ASN cc_start: 0.7747 (t0) cc_final: 0.7295 (t0) REVERT: A 772 GLU cc_start: 0.7348 (tp30) cc_final: 0.7115 (tp30) REVERT: A 858 GLN cc_start: 0.6635 (mm-40) cc_final: 0.6424 (mm-40) REVERT: A 937 ARG cc_start: 0.7170 (mmm-85) cc_final: 0.6774 (mmm-85) REVERT: A 976 TRP cc_start: 0.6782 (m-90) cc_final: 0.6196 (m-90) REVERT: A 1001 VAL cc_start: 0.8027 (m) cc_final: 0.7793 (p) REVERT: A 1056 PHE cc_start: 0.8466 (m-80) cc_final: 0.8201 (m-80) REVERT: A 1144 TYR cc_start: 0.7503 (m-80) cc_final: 0.7273 (m-80) REVERT: A 1147 TYR cc_start: 0.7849 (t80) cc_final: 0.7561 (t80) REVERT: A 1177 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7639 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7545 (m-80) cc_final: 0.6773 (m-80) REVERT: A 1190 MET cc_start: 0.7190 (ttt) cc_final: 0.6636 (ttt) REVERT: A 1198 TYR cc_start: 0.7513 (t80) cc_final: 0.7067 (t80) REVERT: L 79 LYS cc_start: 0.7985 (tttt) cc_final: 0.7738 (tptt) REVERT: H 52 TRP cc_start: 0.7030 (OUTLIER) cc_final: 0.6333 (t-100) REVERT: H 80 TYR cc_start: 0.6909 (m-10) cc_final: 0.6680 (m-10) REVERT: H 103 LEU cc_start: 0.8741 (tp) cc_final: 0.8483 (tp) REVERT: B 136 TYR cc_start: 0.8251 (m-80) cc_final: 0.8010 (m-80) REVERT: B 235 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7544 (mtmm) REVERT: B 259 LYS cc_start: 0.7637 (ptmt) cc_final: 0.7298 (ptmt) REVERT: B 318 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 329 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7582 (tptt) REVERT: B 342 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7489 (t0) REVERT: B 395 THR cc_start: 0.8193 (m) cc_final: 0.7875 (p) REVERT: B 437 LEU cc_start: 0.7906 (mt) cc_final: 0.7517 (mt) REVERT: B 447 PHE cc_start: 0.7761 (m-80) cc_final: 0.7551 (m-10) REVERT: B 478 VAL cc_start: 0.8503 (p) cc_final: 0.8236 (m) REVERT: B 479 TYR cc_start: 0.7627 (p90) cc_final: 0.7373 (p90) REVERT: B 626 ASP cc_start: 0.6980 (t0) cc_final: 0.6413 (t0) REVERT: B 711 ARG cc_start: 0.7446 (mtm180) cc_final: 0.7235 (mtm180) REVERT: B 719 PHE cc_start: 0.8145 (p90) cc_final: 0.7663 (p90) REVERT: B 854 LEU cc_start: 0.8166 (mt) cc_final: 0.7705 (mt) REVERT: B 857 THR cc_start: 0.7507 (p) cc_final: 0.6704 (m) REVERT: B 860 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: B 913 PHE cc_start: 0.7240 (m-80) cc_final: 0.6823 (m-80) REVERT: B 951 LEU cc_start: 0.8557 (mm) cc_final: 0.8353 (mt) REVERT: B 958 ASN cc_start: 0.7709 (m-40) cc_final: 0.7378 (m-40) REVERT: B 1000 ASP cc_start: 0.7370 (t0) cc_final: 0.7071 (t0) REVERT: B 1112 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6817 (mpp) REVERT: B 1139 VAL cc_start: 0.8356 (t) cc_final: 0.8017 (p) REVERT: B 1147 TYR cc_start: 0.7749 (t80) cc_final: 0.7346 (t80) REVERT: B 1181 TYR cc_start: 0.7697 (m-80) cc_final: 0.7358 (m-10) REVERT: B 1182 PHE cc_start: 0.7636 (m-80) cc_final: 0.7307 (m-80) REVERT: B 1189 TRP cc_start: 0.8597 (m100) cc_final: 0.8288 (m100) REVERT: B 1190 MET cc_start: 0.7108 (ttm) cc_final: 0.6668 (ttt) REVERT: B 1198 TYR cc_start: 0.7452 (t80) cc_final: 0.6759 (t80) REVERT: G 32 TYR cc_start: 0.7971 (m-80) cc_final: 0.7451 (m-80) REVERT: G 45 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7403 (mm) REVERT: G 52 TRP cc_start: 0.6652 (OUTLIER) cc_final: 0.5653 (t-100) REVERT: G 103 LEU cc_start: 0.8839 (tp) cc_final: 0.8487 (tp) REVERT: C 180 LEU cc_start: 0.8722 (mt) cc_final: 0.8385 (mm) REVERT: C 235 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7563 (ptpp) REVERT: C 259 LYS cc_start: 0.7655 (ptmt) cc_final: 0.7428 (ptmt) REVERT: C 328 ARG cc_start: 0.6906 (mpt180) cc_final: 0.6138 (mpt180) REVERT: C 329 LYS cc_start: 0.8093 (mttt) cc_final: 0.7561 (ttmm) REVERT: C 342 ASN cc_start: 0.8177 (t0) cc_final: 0.7770 (t0) REVERT: C 566 ASN cc_start: 0.7719 (m-40) cc_final: 0.7286 (p0) REVERT: C 626 ASP cc_start: 0.6359 (t0) cc_final: 0.5547 (t0) REVERT: C 631 LEU cc_start: 0.8706 (mm) cc_final: 0.8140 (mt) REVERT: C 832 GLN cc_start: 0.7910 (mm110) cc_final: 0.7377 (mp10) REVERT: C 999 MET cc_start: 0.6362 (mtp) cc_final: 0.5623 (mtp) REVERT: C 1033 LYS cc_start: 0.8392 (tppt) cc_final: 0.8130 (ttmm) REVERT: C 1039 ASN cc_start: 0.8022 (t0) cc_final: 0.7677 (t0) REVERT: C 1076 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6259 (mp0) REVERT: C 1181 TYR cc_start: 0.7731 (m-80) cc_final: 0.7486 (m-10) REVERT: C 1182 PHE cc_start: 0.7441 (m-80) cc_final: 0.7180 (m-80) REVERT: C 1190 MET cc_start: 0.6941 (ttt) cc_final: 0.6340 (ttt) REVERT: E 84 GLU cc_start: 0.6567 (pp20) cc_final: 0.5991 (pp20) REVERT: I 83 MET cc_start: 0.6871 (pmm) cc_final: 0.6487 (pmm) outliers start: 101 outliers final: 77 residues processed: 943 average time/residue: 0.4161 time to fit residues: 645.3413 Evaluate side-chains 964 residues out of total 3660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 879 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 0.9980 chunk 354 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 342 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A1005 ASN A1097 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 844 ASN B 858 GLN B 860 GLN B1064 GLN ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 315 ASN C 403 ASN C 844 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 GLN ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.139695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113541 restraints weight = 56587.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118053 restraints weight = 29559.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121149 restraints weight = 18284.954| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 34296 Z= 0.260 Angle : 0.699 11.892 46677 Z= 0.360 Chirality : 0.048 0.331 5376 Planarity : 0.004 0.052 5952 Dihedral : 5.914 82.453 5592 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.54 % Allowed : 22.10 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 4176 helix: -0.05 (0.19), residues: 729 sheet: -0.81 (0.15), residues: 1095 loop : -1.19 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 102 HIS 0.015 0.001 HIS L 31 PHE 0.047 0.002 PHE B 122 TYR 0.047 0.002 TYR B 68 ARG 0.008 0.000 ARG C 991 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10068.62 seconds wall clock time: 180 minutes 2.57 seconds (10802.57 seconds total)