Starting phenix.real_space_refine on Thu Feb 22 05:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7po5_13563/02_2024/7po5_13563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7po5_13563/02_2024/7po5_13563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7po5_13563/02_2024/7po5_13563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7po5_13563/02_2024/7po5_13563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7po5_13563/02_2024/7po5_13563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7po5_13563/02_2024/7po5_13563.pdb" } resolution = 3.9 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= 0.036 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 201 5.16 5 C 20940 2.51 5 N 5421 2.21 5 O 6372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32934 Number of models: 1 Model: "" Number of chains: 12 Chain: "Z" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 954 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "X" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 954 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 954 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.32, per 1000 atoms: 0.50 Number of scatterers: 32934 At special positions: 0 Unit cell: (153.36, 150.165, 198.09, 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 201 16.00 O 6372 8.00 N 5421 7.00 C 20940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " 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=2.03 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=2.03 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 X 22 " - pdb=" SG CYS X 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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=2.03 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=2.03 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 H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " 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 NAG-ASN " NAG A1401 " - " ASN A 59 " " NAG A1402 " - " ASN A 146 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 687 " " NAG A1405 " - " ASN A 706 " " NAG B1401 " - " ASN B 59 " " NAG B1402 " - " ASN B 146 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 687 " " NAG B1405 " - " ASN B 706 " " NAG C1401 " - " ASN C 59 " " NAG C1402 " - " ASN C 146 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 687 " " NAG C1405 " - " ASN C 706 " Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 6.4 seconds 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 75 sheets defined 22.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'Z' and resid 60 through 64 removed outlier: 3.702A pdb=" N LYS Z 64 " --> pdb=" O PRO Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 90 removed outlier: 3.671A pdb=" N THR Z 90 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.094A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.583A pdb=" N LYS B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.603A pdb=" N THR B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.526A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 removed outlier: 3.958A pdb=" N GLY B 388 " --> pdb=" O LYS B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.829A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.613A pdb=" N SER B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 817 through 823 removed outlier: 3.598A pdb=" N CYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.581A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 877 Processing helix chain 'B' and resid 906 through 916 removed outlier: 4.007A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 938 through 946 Processing helix chain 'B' and resid 956 through 970 Processing helix chain 'B' and resid 976 through 980 removed outlier: 3.829A pdb=" N ALA B 980 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 999 through 1004 removed outlier: 4.121A pdb=" N GLN B1004 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1023 Processing helix chain 'B' and resid 1028 through 1051 Processing helix chain 'B' and resid 1052 through 1054 No H-bonds generated for 'chain 'B' and resid 1052 through 1054' Processing helix chain 'B' and resid 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1119 removed outlier: 3.634A pdb=" N ALA B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1207 removed outlier: 3.617A pdb=" N ASN B1206 " --> pdb=" O THR B1203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B1207 " --> pdb=" O GLU B1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1203 through 1207' Processing helix chain 'X' and resid 60 through 64 removed outlier: 3.703A pdb=" N LYS X 64 " --> pdb=" O PRO X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 90 removed outlier: 3.670A pdb=" N THR X 90 " --> pdb=" O ALA X 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.093A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.613A pdb=" N LYS C 92 " --> pdb=" O LEU C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.605A pdb=" N THR C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 363 through 371 removed outlier: 4.037A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 removed outlier: 3.995A pdb=" N GLY C 388 " --> pdb=" O LYS C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.799A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.665A pdb=" N SER C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'C' and resid 565 through 568 Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 817 through 823 removed outlier: 3.543A pdb=" N CYS C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 833 Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.588A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 877 Processing helix chain 'C' and resid 906 through 916 removed outlier: 3.991A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 938 through 946 Processing helix chain 'C' and resid 956 through 970 Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.512A pdb=" N ALA C 979 " --> pdb=" O TRP C 976 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 980 " --> pdb=" O THR C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 999 through 1004 removed outlier: 4.046A pdb=" N GLN C1004 " --> pdb=" O ASP C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 Processing helix chain 'C' and resid 1028 through 1051 Processing helix chain 'C' and resid 1052 through 1054 No H-bonds generated for 'chain 'C' and resid 1052 through 1054' Processing helix chain 'C' and resid 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1119 removed outlier: 3.605A pdb=" N ALA C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1207 removed outlier: 3.617A pdb=" N ASN C1206 " --> pdb=" O THR C1203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C1207 " --> pdb=" O GLU C1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1203 through 1207' Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.706A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.673A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.087A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.587A pdb=" N LYS A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.635A pdb=" N THR A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.516A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 removed outlier: 3.911A pdb=" N GLY A 388 " --> pdb=" O LYS A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.893A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.620A pdb=" N SER A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 565 through 568 removed outlier: 3.502A pdb=" N CYS A 568 " --> pdb=" O GLY A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.575A pdb=" N CYS A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.612A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 877 Processing helix chain 'A' and resid 906 through 916 removed outlier: 4.010A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 938 through 946 Processing helix chain 'A' and resid 956 through 970 Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.518A pdb=" N ALA A 979 " --> pdb=" O TRP A 976 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 980 " --> pdb=" O THR A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 980' Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 4.060A pdb=" N GLN A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 Processing helix chain 'A' and resid 1028 through 1051 Processing helix chain 'A' and resid 1052 through 1054 No H-bonds generated for 'chain 'A' and resid 1052 through 1054' Processing helix chain 'A' and resid 1062 through 1070 Processing helix chain 'A' and resid 1071 through 1119 removed outlier: 3.558A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 3.604A pdb=" N ASN A1206 " --> pdb=" O THR A1203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1207 " --> pdb=" O GLU A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1207' Processing sheet with id=AA1, first strand: chain 'Z' and resid 4 through 7 removed outlier: 3.775A pdb=" N THR Z 21 " --> pdb=" O TRP Z 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 51 through 52 removed outlier: 3.687A pdb=" N TYR Z 33 " --> pdb=" O GLY Z 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.775A pdb=" N SER D 7 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.292A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.537A pdb=" N SER B 37 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.635A pdb=" N GLY B 66 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.845A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR A 669 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 634 " --> pdb=" O VAL A 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.735A pdb=" N TYR B 249 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 189 removed outlier: 7.719A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 310 through 311 removed outlier: 3.795A pdb=" N SER B 681 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 719 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 324 through 327 removed outlier: 3.680A pdb=" N GLY B 634 " --> pdb=" O VAL B 623 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 669 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 650 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.770A pdb=" N GLU B 353 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 362 " --> pdb=" O CYS B 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.770A pdb=" N GLU B 353 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 391 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 600 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AB9, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.756A pdb=" N THR B 543 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AC2, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.505A pdb=" N GLY B 564 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 730 through 737 removed outlier: 6.839A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 777 through 779 removed outlier: 6.006A pdb=" N ASN B 777 " --> pdb=" O LEU C 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.381A pdb=" N GLU B 791 " --> pdb=" O ARG B1162 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B1162 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 793 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B1160 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B1158 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU B 797 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B1152 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 805 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 813 through 815 removed outlier: 4.218A pdb=" N LYS B 813 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 949 " --> pdb=" O THR B 815 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 870 through 872 Processing sheet with id=AC8, first strand: chain 'B' and resid 1167 through 1168 Processing sheet with id=AC9, first strand: chain 'B' and resid 1180 through 1185 removed outlier: 3.564A pdb=" N THR B1192 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.754A pdb=" N THR X 21 " --> pdb=" O TRP X 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 51 through 52 removed outlier: 3.700A pdb=" N TYR X 33 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.734A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.316A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.528A pdb=" N SER C 37 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.642A pdb=" N GLY C 66 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.515A pdb=" N SER C 97 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 249 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AE2, first strand: chain 'C' and resid 187 through 189 removed outlier: 7.737A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 310 through 311 removed outlier: 3.650A pdb=" N PHE C 719 " --> pdb=" O VAL C 726 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.686A pdb=" N GLY C 634 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR C 669 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 650 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.778A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 355 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 362 " --> pdb=" O CYS C 606 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.778A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 355 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 391 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 600 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AE8, first strand: chain 'C' and resid 484 through 485 removed outlier: 3.779A pdb=" N THR C 543 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AF1, first strand: chain 'C' and resid 563 through 564 Processing sheet with id=AF2, first strand: chain 'C' and resid 730 through 737 removed outlier: 10.283A pdb=" N TYR C 766 " --> pdb=" O ASN C 731 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N THR C 733 " --> pdb=" O TYR C 766 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE C 768 " --> pdb=" O THR C 733 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 735 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 777 through 779 removed outlier: 5.994A pdb=" N ASN C 777 " --> pdb=" O LEU A 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.384A pdb=" N GLU C 791 " --> pdb=" O ARG C1162 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG C1162 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN C 793 " --> pdb=" O THR C1160 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR C1160 " --> pdb=" O GLN C 793 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR C1158 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 797 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 805 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 813 through 816 removed outlier: 4.210A pdb=" N LYS C 813 " --> pdb=" O LEU C 951 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1167 through 1168 removed outlier: 3.508A pdb=" N LEU C1167 " --> pdb=" O ILE C1175 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1180 through 1185 removed outlier: 3.560A pdb=" N THR C1192 " --> pdb=" O TYR C1181 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.794A pdb=" N THR H 21 " --> pdb=" O TRP H 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 51 through 52 removed outlier: 3.690A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.786A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AG5, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.544A pdb=" N SER A 37 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 238 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.623A pdb=" N GLY A 66 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.507A pdb=" N SER A 97 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 249 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AG9, first strand: chain 'A' and resid 187 through 189 removed outlier: 7.678A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.690A pdb=" N PHE A 719 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.790A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 362 " --> pdb=" O CYS A 606 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.790A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 391 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 600 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 437 " --> pdb=" O CYS A 589 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AH5, first strand: chain 'A' and resid 484 through 485 removed outlier: 3.782A pdb=" N THR A 543 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AH7, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.514A pdb=" N GLY A 564 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 730 through 737 removed outlier: 6.923A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.391A pdb=" N GLU A 791 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG A1162 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN A 793 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A1160 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR A1158 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 797 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 805 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A1145 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A1142 " --> pdb=" O GLY A1145 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.218A pdb=" N LYS A 813 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 949 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 3.591A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'A' and resid 1180 through 1185 removed outlier: 3.531A pdb=" N THR A1192 " --> pdb=" O TYR A1181 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3162 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: 15.33 Time building geometry restraints manager: 12.69 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: 10515 1.34 - 1.47: 8542 1.47 - 1.59: 14372 1.59 - 1.71: 0 1.71 - 1.83: 261 Bond restraints: 33690 Sorted by residual: bond pdb=" C1 NAG B1405 " pdb=" O5 NAG B1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 33685 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.81: 854 106.81 - 113.62: 18188 113.62 - 120.44: 12356 120.44 - 127.25: 14214 127.25 - 134.07: 258 Bond angle restraints: 45870 Sorted by residual: angle pdb=" C GLY C1130 " pdb=" N ASN C1131 " pdb=" CA ASN C1131 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C GLY B1130 " pdb=" N ASN B1131 " pdb=" CA ASN B1131 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C GLY A1130 " pdb=" N ASN A1131 " pdb=" CA ASN A1131 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN C 379 " pdb=" N ASN C 380 " pdb=" CA ASN C 380 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 angle pdb=" C ASN A 379 " pdb=" N ASN A 380 " pdb=" CA ASN A 380 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 ... (remaining 45865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 18953 22.36 - 44.73: 1089 44.73 - 67.09: 121 67.09 - 89.46: 18 89.46 - 111.82: 9 Dihedral angle restraints: 20190 sinusoidal: 7920 harmonic: 12270 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 169 " pdb=" CB CYS B 169 " ideal model delta sinusoidal sigma weight residual 93.00 154.77 -61.77 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CB CYS C 21 " pdb=" SG CYS C 21 " pdb=" SG CYS C 169 " pdb=" CB CYS C 169 " ideal model delta sinusoidal sigma weight residual 93.00 154.38 -61.38 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual 93.00 153.98 -60.98 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 20187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 5016 0.112 - 0.223: 174 0.223 - 0.335: 3 0.335 - 0.446: 0 0.446 - 0.558: 3 Chirality restraints: 5196 Sorted by residual: chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C1 NAG A1402 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A1402 " pdb=" O5 NAG A1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.64e+00 ... (remaining 5193 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 889 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO A 890 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 889 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO C 890 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 890 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 890 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 889 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 890 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.040 5.00e-02 4.00e+02 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8695 2.80 - 3.33: 26609 3.33 - 3.85: 54551 3.85 - 4.38: 60558 4.38 - 4.90: 107492 Nonbonded interactions: 257905 Sorted by model distance: nonbonded pdb=" OG SER A 348 " pdb=" OD1 ASN A 351 " model vdw 2.277 2.440 nonbonded pdb=" OG SER B 348 " pdb=" OD1 ASN B 351 " model vdw 2.281 2.440 nonbonded pdb=" OG SER C 348 " pdb=" OD1 ASN C 351 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR B 990 " pdb=" O PRO A1177 " model vdw 2.288 2.440 nonbonded pdb=" O VAL B 639 " pdb=" OG1 THR B 669 " model vdw 2.303 2.440 ... (remaining 257900 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 'F' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.030 Extract box with map and model: 8.390 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 86.050 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.200 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 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 : 0.003 0.101 33690 Z= 0.220 Angle : 0.650 9.337 45870 Z= 0.356 Chirality : 0.049 0.558 5196 Planarity : 0.006 0.072 5889 Dihedral : 13.442 111.819 12159 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4170 helix: -1.28 (0.15), residues: 816 sheet: -0.43 (0.17), residues: 990 loop : -1.34 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.004 0.001 HIS B 215 PHE 0.016 0.002 PHE A 399 TYR 0.022 0.001 TYR C 317 ARG 0.003 0.000 ARG C 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1176 time to evaluate : 3.692 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ILE cc_start: 0.7935 (mm) cc_final: 0.7718 (mt) REVERT: B 75 TYR cc_start: 0.7791 (m-10) cc_final: 0.7581 (m-80) REVERT: B 88 ARG cc_start: 0.7314 (mtt90) cc_final: 0.7005 (mtt90) REVERT: B 213 TYR cc_start: 0.7854 (m-80) cc_final: 0.7573 (m-10) REVERT: B 261 THR cc_start: 0.7367 (m) cc_final: 0.6587 (p) REVERT: B 279 ASN cc_start: 0.7171 (p0) cc_final: 0.6756 (p0) REVERT: B 299 LYS cc_start: 0.7340 (mttt) cc_final: 0.6929 (mttt) REVERT: B 301 LYS cc_start: 0.7889 (tptp) cc_final: 0.7573 (tptm) REVERT: B 318 THR cc_start: 0.7075 (m) cc_final: 0.6736 (t) REVERT: B 359 ASN cc_start: 0.7990 (m-40) cc_final: 0.7785 (m-40) REVERT: B 368 MET cc_start: 0.6264 (mtm) cc_final: 0.5797 (mtm) REVERT: B 379 ASN cc_start: 0.6958 (t0) cc_final: 0.6733 (t0) REVERT: B 382 ASP cc_start: 0.7620 (p0) cc_final: 0.7336 (p0) REVERT: B 389 MET cc_start: 0.3579 (ptp) cc_final: 0.3221 (ptp) REVERT: B 398 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7734 (ttpp) REVERT: B 471 VAL cc_start: 0.8170 (m) cc_final: 0.7692 (p) REVERT: B 559 LYS cc_start: 0.7658 (pttt) cc_final: 0.7394 (pttt) REVERT: B 590 ASN cc_start: 0.7632 (m-40) cc_final: 0.6920 (m-40) REVERT: B 607 SER cc_start: 0.7004 (p) cc_final: 0.6803 (p) REVERT: B 626 ASP cc_start: 0.6671 (t0) cc_final: 0.6437 (t0) REVERT: B 673 ARG cc_start: 0.6876 (mtp85) cc_final: 0.6326 (ttm110) REVERT: B 731 ASN cc_start: 0.6499 (t0) cc_final: 0.6292 (t0) REVERT: B 768 PHE cc_start: 0.7644 (t80) cc_final: 0.7441 (t80) REVERT: B 802 ASN cc_start: 0.6693 (p0) cc_final: 0.6441 (p0) REVERT: B 906 SER cc_start: 0.7614 (p) cc_final: 0.7181 (t) REVERT: B 925 GLU cc_start: 0.6482 (tt0) cc_final: 0.6092 (tt0) REVERT: B 928 ASN cc_start: 0.7874 (m-40) cc_final: 0.7661 (m110) REVERT: B 946 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7584 (mmtm) REVERT: B 1033 LYS cc_start: 0.7280 (mtpp) cc_final: 0.7041 (mtpp) REVERT: B 1035 GLN cc_start: 0.6968 (mm-40) cc_final: 0.5895 (mm-40) REVERT: B 1046 ASN cc_start: 0.6107 (t0) cc_final: 0.5806 (t0) REVERT: B 1049 LEU cc_start: 0.7830 (tp) cc_final: 0.6809 (tt) REVERT: B 1069 ARG cc_start: 0.6908 (mtp180) cc_final: 0.6698 (ttm170) REVERT: B 1073 LEU cc_start: 0.7304 (tt) cc_final: 0.7059 (pt) REVERT: B 1106 PHE cc_start: 0.6387 (t80) cc_final: 0.6089 (t80) REVERT: B 1112 MET cc_start: 0.6174 (mtp) cc_final: 0.5730 (mtp) REVERT: B 1118 CYS cc_start: 0.5281 (m) cc_final: 0.4655 (m) REVERT: B 1187 ASN cc_start: 0.7674 (m-40) cc_final: 0.7135 (t0) REVERT: C 24 ASP cc_start: 0.7298 (t0) cc_final: 0.7083 (t0) REVERT: C 88 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6840 (mtt90) REVERT: C 98 ASP cc_start: 0.7165 (p0) cc_final: 0.6874 (p0) REVERT: C 114 LYS cc_start: 0.7510 (tttm) cc_final: 0.7293 (tttm) REVERT: C 136 TYR cc_start: 0.7074 (m-80) cc_final: 0.6599 (m-80) REVERT: C 206 ASP cc_start: 0.6529 (t70) cc_final: 0.6324 (p0) REVERT: C 275 LEU cc_start: 0.7869 (tp) cc_final: 0.7619 (tt) REVERT: C 279 ASN cc_start: 0.7200 (p0) cc_final: 0.6510 (p0) REVERT: C 280 GLN cc_start: 0.6436 (mm-40) cc_final: 0.6210 (mm110) REVERT: C 285 PHE cc_start: 0.8215 (p90) cc_final: 0.7979 (p90) REVERT: C 301 LYS cc_start: 0.8027 (tptp) cc_final: 0.7673 (tppt) REVERT: C 313 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6256 (mm-30) REVERT: C 314 LEU cc_start: 0.7344 (mt) cc_final: 0.6954 (mt) REVERT: C 318 THR cc_start: 0.7200 (m) cc_final: 0.6967 (t) REVERT: C 477 VAL cc_start: 0.8109 (t) cc_final: 0.7862 (p) REVERT: C 590 ASN cc_start: 0.7617 (m-40) cc_final: 0.7109 (m-40) REVERT: C 602 SER cc_start: 0.7347 (t) cc_final: 0.6889 (t) REVERT: C 624 ASN cc_start: 0.7457 (m-40) cc_final: 0.6834 (m-40) REVERT: C 645 ASN cc_start: 0.5603 (m-40) cc_final: 0.5378 (m-40) REVERT: C 679 ARG cc_start: 0.6618 (ttt180) cc_final: 0.6240 (ttt180) REVERT: C 684 PHE cc_start: 0.7627 (t80) cc_final: 0.7349 (t80) REVERT: C 888 PHE cc_start: 0.7181 (m-10) cc_final: 0.6860 (m-80) REVERT: C 913 PHE cc_start: 0.6645 (m-80) cc_final: 0.6443 (m-80) REVERT: C 923 PHE cc_start: 0.6877 (m-10) cc_final: 0.6521 (m-80) REVERT: C 927 TYR cc_start: 0.6885 (m-10) cc_final: 0.6513 (m-80) REVERT: C 928 ASN cc_start: 0.7828 (m-40) cc_final: 0.7491 (m110) REVERT: C 946 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7721 (mmtm) REVERT: C 948 ILE cc_start: 0.6930 (mm) cc_final: 0.6444 (mm) REVERT: C 969 SER cc_start: 0.7839 (m) cc_final: 0.7537 (p) REVERT: C 989 GLN cc_start: 0.7387 (tt0) cc_final: 0.6314 (tt0) REVERT: C 999 MET cc_start: 0.6927 (mmm) cc_final: 0.6409 (mmm) REVERT: C 1009 ILE cc_start: 0.7714 (tp) cc_final: 0.6923 (tp) REVERT: C 1013 PHE cc_start: 0.6488 (m-80) cc_final: 0.6155 (m-80) REVERT: C 1035 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6296 (mm-40) REVERT: C 1049 LEU cc_start: 0.8023 (tp) cc_final: 0.7782 (tt) REVERT: C 1052 LEU cc_start: 0.8110 (mt) cc_final: 0.7872 (mt) REVERT: C 1069 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6863 (ttp-110) REVERT: C 1082 LEU cc_start: 0.7972 (mt) cc_final: 0.7680 (mm) REVERT: C 1113 GLU cc_start: 0.6251 (tt0) cc_final: 0.5892 (tt0) REVERT: C 1114 LYS cc_start: 0.6472 (mttm) cc_final: 0.6246 (mttm) REVERT: C 1124 SER cc_start: 0.7567 (p) cc_final: 0.6877 (p) REVERT: C 1135 ILE cc_start: 0.8216 (mt) cc_final: 0.7919 (mp) REVERT: C 1150 HIS cc_start: 0.6562 (m-70) cc_final: 0.6267 (m-70) REVERT: A 119 TYR cc_start: 0.6402 (m-80) cc_final: 0.6057 (m-80) REVERT: A 274 TYR cc_start: 0.7630 (m-10) cc_final: 0.7269 (m-10) REVERT: A 279 ASN cc_start: 0.7126 (p0) cc_final: 0.6695 (p0) REVERT: A 313 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6187 (mm-30) REVERT: A 346 VAL cc_start: 0.8169 (p) cc_final: 0.7802 (m) REVERT: A 359 ASN cc_start: 0.7669 (m-40) cc_final: 0.7272 (m-40) REVERT: A 378 CYS cc_start: 0.4931 (m) cc_final: 0.4572 (m) REVERT: A 379 ASN cc_start: 0.6954 (t0) cc_final: 0.6750 (t0) REVERT: A 543 THR cc_start: 0.8120 (m) cc_final: 0.7807 (p) REVERT: A 559 LYS cc_start: 0.7438 (pttt) cc_final: 0.7170 (pttt) REVERT: A 590 ASN cc_start: 0.7773 (m-40) cc_final: 0.6390 (m-40) REVERT: A 602 SER cc_start: 0.7565 (t) cc_final: 0.7210 (p) REVERT: A 610 LEU cc_start: 0.7734 (mm) cc_final: 0.7513 (mt) REVERT: A 624 ASN cc_start: 0.7598 (m-40) cc_final: 0.6177 (m-40) REVERT: A 631 LEU cc_start: 0.8510 (mt) cc_final: 0.8059 (mt) REVERT: A 720 ASP cc_start: 0.6955 (m-30) cc_final: 0.6565 (m-30) REVERT: A 774 PHE cc_start: 0.7943 (m-80) cc_final: 0.7458 (m-80) REVERT: A 838 SER cc_start: 0.7888 (t) cc_final: 0.7625 (t) REVERT: A 906 SER cc_start: 0.7945 (p) cc_final: 0.7579 (t) REVERT: A 923 PHE cc_start: 0.6705 (m-10) cc_final: 0.6499 (m-80) REVERT: A 927 TYR cc_start: 0.6966 (m-10) cc_final: 0.6398 (m-80) REVERT: A 946 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7921 (mmtm) REVERT: A 1035 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6255 (mm-40) REVERT: A 1052 LEU cc_start: 0.8042 (mt) cc_final: 0.7821 (mt) REVERT: A 1082 LEU cc_start: 0.7880 (mt) cc_final: 0.7596 (mp) REVERT: A 1106 PHE cc_start: 0.6496 (t80) cc_final: 0.6231 (t80) REVERT: A 1198 TYR cc_start: 0.7737 (t80) cc_final: 0.7418 (t80) outliers start: 1 outliers final: 1 residues processed: 1176 average time/residue: 0.4574 time to fit residues: 850.9477 Evaluate side-chains 1004 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1003 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 802 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 0.8980 chunk 316 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 326 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 378 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 380 ASN B 481 GLN B 573 GLN B 590 ASN B 648 GLN B 649 ASN B 707 ASN ** B 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 585 GLN C 590 ASN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 ASN ** C1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1127 ASN ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 280 GLN A 573 GLN A 585 GLN A 590 ASN A 649 ASN A 731 ASN A 802 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A1127 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 33690 Z= 0.339 Angle : 0.652 11.226 45870 Z= 0.354 Chirality : 0.048 0.496 5196 Planarity : 0.005 0.054 5889 Dihedral : 6.412 99.680 4889 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.28 % Allowed : 11.71 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4170 helix: 0.21 (0.18), residues: 786 sheet: -0.54 (0.15), residues: 1107 loop : -1.02 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 452 HIS 0.005 0.001 HIS B 598 PHE 0.026 0.002 PHE B 595 TYR 0.024 0.002 TYR B 676 ARG 0.010 0.001 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1035 time to evaluate : 3.410 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: B 16 ILE cc_start: 0.8061 (mm) cc_final: 0.7841 (mt) REVERT: B 28 ASP cc_start: 0.6898 (t0) cc_final: 0.6680 (t0) REVERT: B 88 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7178 (mtt90) REVERT: B 106 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7832 (ttpp) REVERT: B 119 TYR cc_start: 0.6617 (m-80) cc_final: 0.6299 (m-80) REVERT: B 206 ASP cc_start: 0.7093 (t0) cc_final: 0.6802 (t70) REVERT: B 213 TYR cc_start: 0.7991 (m-80) cc_final: 0.7696 (m-10) REVERT: B 252 MET cc_start: 0.6531 (mpp) cc_final: 0.6248 (mpp) REVERT: B 262 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (mt) REVERT: B 279 ASN cc_start: 0.7555 (p0) cc_final: 0.7214 (p0) REVERT: B 280 GLN cc_start: 0.7460 (pm20) cc_final: 0.7156 (pm20) REVERT: B 299 LYS cc_start: 0.7718 (mttt) cc_final: 0.7301 (mttt) REVERT: B 318 THR cc_start: 0.7428 (m) cc_final: 0.6976 (t) REVERT: B 359 ASN cc_start: 0.8095 (m-40) cc_final: 0.7756 (m-40) REVERT: B 379 ASN cc_start: 0.7113 (t0) cc_final: 0.6857 (t0) REVERT: B 398 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7788 (ttpp) REVERT: B 403 ASN cc_start: 0.7385 (t0) cc_final: 0.7134 (t0) REVERT: B 471 VAL cc_start: 0.8213 (m) cc_final: 0.7942 (p) REVERT: B 559 LYS cc_start: 0.7903 (pttt) cc_final: 0.7693 (pttt) REVERT: B 573 GLN cc_start: 0.7454 (mm110) cc_final: 0.7147 (mp10) REVERT: B 635 ILE cc_start: 0.8080 (mp) cc_final: 0.7753 (pt) REVERT: B 671 MET cc_start: 0.7191 (mmm) cc_final: 0.6976 (mmm) REVERT: B 673 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6751 (ttm110) REVERT: B 768 PHE cc_start: 0.7819 (t80) cc_final: 0.7485 (t80) REVERT: B 1033 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7358 (mtpp) REVERT: B 1035 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6557 (mm-40) REVERT: B 1039 ASN cc_start: 0.6644 (m-40) cc_final: 0.5219 (m-40) REVERT: B 1043 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5919 (mt-10) REVERT: B 1076 GLU cc_start: 0.5678 (mt-10) cc_final: 0.5404 (mt-10) REVERT: B 1112 MET cc_start: 0.6493 (mtp) cc_final: 0.5957 (mtp) REVERT: B 1187 ASN cc_start: 0.7867 (m-40) cc_final: 0.7414 (t0) REVERT: C 24 ASP cc_start: 0.7437 (t0) cc_final: 0.7180 (t0) REVERT: C 41 VAL cc_start: 0.8142 (t) cc_final: 0.7735 (p) REVERT: C 114 LYS cc_start: 0.7753 (tttm) cc_final: 0.7527 (tttm) REVERT: C 136 TYR cc_start: 0.7103 (m-80) cc_final: 0.6520 (m-80) REVERT: C 206 ASP cc_start: 0.6966 (t70) cc_final: 0.6593 (p0) REVERT: C 295 MET cc_start: 0.6170 (tpt) cc_final: 0.5818 (tpt) REVERT: C 299 LYS cc_start: 0.7607 (mttt) cc_final: 0.7228 (mttt) REVERT: C 318 THR cc_start: 0.7623 (m) cc_final: 0.7146 (t) REVERT: C 437 LEU cc_start: 0.8117 (mt) cc_final: 0.7889 (mt) REVERT: C 543 THR cc_start: 0.8158 (m) cc_final: 0.7904 (p) REVERT: C 602 SER cc_start: 0.7368 (t) cc_final: 0.7158 (t) REVERT: C 631 LEU cc_start: 0.8509 (mt) cc_final: 0.8271 (mt) REVERT: C 673 ARG cc_start: 0.7047 (mtp85) cc_final: 0.6812 (ttm110) REVERT: C 698 ILE cc_start: 0.8588 (mt) cc_final: 0.8277 (mt) REVERT: C 702 TYR cc_start: 0.8522 (t80) cc_final: 0.8293 (t80) REVERT: C 731 ASN cc_start: 0.6569 (t0) cc_final: 0.6267 (t0) REVERT: C 738 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7334 (mm110) REVERT: C 915 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7882 (mmmt) REVERT: C 918 LEU cc_start: 0.7608 (mt) cc_final: 0.7350 (mm) REVERT: C 923 PHE cc_start: 0.7470 (m-10) cc_final: 0.7006 (m-80) REVERT: C 927 TYR cc_start: 0.7272 (m-80) cc_final: 0.6773 (m-80) REVERT: C 946 LYS cc_start: 0.8338 (mmtp) cc_final: 0.7959 (mmtm) REVERT: C 989 GLN cc_start: 0.7500 (tt0) cc_final: 0.6487 (tt0) REVERT: C 999 MET cc_start: 0.7199 (mmm) cc_final: 0.6617 (mmm) REVERT: C 1009 ILE cc_start: 0.7879 (tp) cc_final: 0.7160 (tp) REVERT: C 1013 PHE cc_start: 0.6842 (m-80) cc_final: 0.6373 (m-80) REVERT: C 1035 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6873 (mm-40) REVERT: C 1039 ASN cc_start: 0.6695 (m-40) cc_final: 0.6489 (m-40) REVERT: C 1073 LEU cc_start: 0.7767 (pt) cc_final: 0.7502 (pp) REVERT: C 1083 ILE cc_start: 0.7659 (mt) cc_final: 0.7327 (mm) REVERT: C 1113 GLU cc_start: 0.6320 (tt0) cc_final: 0.6038 (tt0) REVERT: C 1124 SER cc_start: 0.7270 (p) cc_final: 0.7036 (p) REVERT: C 1157 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7086 (mmmt) REVERT: C 1165 PRO cc_start: 0.7233 (Cg_endo) cc_final: 0.6988 (Cg_exo) REVERT: C 1210 MET cc_start: 0.6010 (tpt) cc_final: 0.5524 (mmm) REVERT: A 28 ASP cc_start: 0.7684 (t0) cc_final: 0.7433 (t0) REVERT: A 108 LYS cc_start: 0.8046 (tttt) cc_final: 0.7728 (tttt) REVERT: A 136 TYR cc_start: 0.7328 (m-80) cc_final: 0.6905 (m-80) REVERT: A 206 ASP cc_start: 0.7260 (t0) cc_final: 0.7039 (t70) REVERT: A 274 TYR cc_start: 0.7516 (m-10) cc_final: 0.7277 (m-10) REVERT: A 279 ASN cc_start: 0.7553 (p0) cc_final: 0.7328 (p0) REVERT: A 301 LYS cc_start: 0.8160 (tppt) cc_final: 0.7943 (tptm) REVERT: A 313 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6598 (mm-30) REVERT: A 318 THR cc_start: 0.7632 (m) cc_final: 0.7050 (t) REVERT: A 346 VAL cc_start: 0.7998 (p) cc_final: 0.7752 (m) REVERT: A 359 ASN cc_start: 0.7889 (m-40) cc_final: 0.7501 (m-40) REVERT: A 364 MET cc_start: 0.5785 (mmm) cc_final: 0.5552 (tmm) REVERT: A 368 MET cc_start: 0.6590 (mtm) cc_final: 0.6115 (mtm) REVERT: A 401 ILE cc_start: 0.8290 (mm) cc_final: 0.8017 (mt) REVERT: A 420 PHE cc_start: 0.7601 (m-10) cc_final: 0.7234 (m-10) REVERT: A 543 THR cc_start: 0.8180 (m) cc_final: 0.7894 (p) REVERT: A 610 LEU cc_start: 0.7819 (mm) cc_final: 0.7516 (mt) REVERT: A 644 TYR cc_start: 0.7051 (m-80) cc_final: 0.6532 (m-80) REVERT: A 649 ASN cc_start: 0.7743 (m-40) cc_final: 0.7527 (m-40) REVERT: A 671 MET cc_start: 0.7241 (mmm) cc_final: 0.6928 (mmm) REVERT: A 720 ASP cc_start: 0.7476 (m-30) cc_final: 0.6749 (m-30) REVERT: A 838 SER cc_start: 0.8017 (t) cc_final: 0.7601 (t) REVERT: A 888 PHE cc_start: 0.7331 (m-10) cc_final: 0.7094 (m-80) REVERT: A 923 PHE cc_start: 0.7301 (m-10) cc_final: 0.7093 (m-80) REVERT: A 949 LYS cc_start: 0.7544 (ttmm) cc_final: 0.7279 (ttmm) REVERT: A 957 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5771 (mm-30) REVERT: A 999 MET cc_start: 0.6524 (ttp) cc_final: 0.5865 (ttp) REVERT: A 1035 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6653 (tp40) REVERT: A 1127 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7137 (m110) outliers start: 83 outliers final: 54 residues processed: 1064 average time/residue: 0.4646 time to fit residues: 785.5921 Evaluate side-chains 1009 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 952 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 738 GLN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 778 SER Chi-restraints excluded: chain C residue 843 ILE Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1066 ILE Chi-restraints excluded: chain C residue 1127 ASN Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1127 ASN Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 210 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 315 optimal weight: 4.9990 chunk 257 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 379 optimal weight: 0.5980 chunk 409 optimal weight: 1.9990 chunk 337 optimal weight: 0.7980 chunk 376 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 585 GLN B 851 ASN ** B1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 ASN ** B1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 89 GLN C 248 HIS C 573 GLN C 648 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN L 6 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 475 HIS A 585 GLN A 731 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33690 Z= 0.210 Angle : 0.580 9.690 45870 Z= 0.312 Chirality : 0.046 0.437 5196 Planarity : 0.004 0.051 5889 Dihedral : 6.026 94.795 4887 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.69 % Allowed : 15.77 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4170 helix: 0.79 (0.19), residues: 768 sheet: -0.27 (0.16), residues: 1068 loop : -1.03 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 35 HIS 0.005 0.001 HIS B1134 PHE 0.020 0.002 PHE A 774 TYR 0.026 0.002 TYR A 718 ARG 0.011 0.001 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1002 time to evaluate : 3.257 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: B 16 ILE cc_start: 0.8068 (mm) cc_final: 0.7866 (mt) REVERT: B 75 TYR cc_start: 0.8038 (m-80) cc_final: 0.7824 (m-80) REVERT: B 108 LYS cc_start: 0.7969 (tttt) cc_final: 0.7577 (tttt) REVERT: B 111 LYS cc_start: 0.7663 (mttm) cc_final: 0.7402 (mttp) REVERT: B 119 TYR cc_start: 0.6503 (m-80) cc_final: 0.6295 (m-80) REVERT: B 206 ASP cc_start: 0.6979 (t0) cc_final: 0.6727 (t70) REVERT: B 213 TYR cc_start: 0.7907 (m-80) cc_final: 0.7620 (m-10) REVERT: B 222 THR cc_start: 0.7691 (p) cc_final: 0.7490 (p) REVERT: B 252 MET cc_start: 0.6464 (mpp) cc_final: 0.6237 (mpp) REVERT: B 262 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7776 (mt) REVERT: B 279 ASN cc_start: 0.7518 (p0) cc_final: 0.7296 (p0) REVERT: B 295 MET cc_start: 0.6130 (tpt) cc_final: 0.5820 (tpt) REVERT: B 299 LYS cc_start: 0.7642 (mttt) cc_final: 0.7109 (mttt) REVERT: B 318 THR cc_start: 0.7459 (m) cc_final: 0.7010 (t) REVERT: B 380 ASN cc_start: 0.7832 (m110) cc_final: 0.7278 (m-40) REVERT: B 398 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7822 (ttpp) REVERT: B 484 PHE cc_start: 0.6927 (m-80) cc_final: 0.6296 (m-80) REVERT: B 573 GLN cc_start: 0.7575 (mm110) cc_final: 0.7343 (mp10) REVERT: B 624 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 635 ILE cc_start: 0.8102 (mp) cc_final: 0.7725 (pt) REVERT: B 671 MET cc_start: 0.7174 (mmm) cc_final: 0.6942 (mmm) REVERT: B 673 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6689 (ttm110) REVERT: B 709 LEU cc_start: 0.7931 (mt) cc_final: 0.7702 (mp) REVERT: B 714 GLN cc_start: 0.7441 (tp40) cc_final: 0.6939 (tm-30) REVERT: B 768 PHE cc_start: 0.7654 (t80) cc_final: 0.7400 (t80) REVERT: B 866 MET cc_start: 0.6449 (tpp) cc_final: 0.6202 (mpp) REVERT: B 918 LEU cc_start: 0.7225 (mt) cc_final: 0.6971 (mp) REVERT: B 1035 GLN cc_start: 0.6926 (mm-40) cc_final: 0.6423 (mm-40) REVERT: B 1039 ASN cc_start: 0.6560 (m-40) cc_final: 0.5141 (m-40) REVERT: B 1110 GLN cc_start: 0.7003 (tp-100) cc_final: 0.6700 (tp40) REVERT: B 1187 ASN cc_start: 0.7782 (m-40) cc_final: 0.7392 (t0) REVERT: C 24 ASP cc_start: 0.7444 (t0) cc_final: 0.7138 (t0) REVERT: C 41 VAL cc_start: 0.8171 (t) cc_final: 0.7701 (p) REVERT: C 88 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6993 (mtt90) REVERT: C 136 TYR cc_start: 0.7019 (m-80) cc_final: 0.6469 (m-80) REVERT: C 206 ASP cc_start: 0.6867 (t70) cc_final: 0.6532 (p0) REVERT: C 279 ASN cc_start: 0.7357 (p0) cc_final: 0.6967 (p0) REVERT: C 295 MET cc_start: 0.6121 (tpt) cc_final: 0.5785 (tpt) REVERT: C 299 LYS cc_start: 0.7454 (mttt) cc_final: 0.6910 (mttt) REVERT: C 363 ASN cc_start: 0.4565 (OUTLIER) cc_final: 0.3446 (p0) REVERT: C 437 LEU cc_start: 0.8131 (mt) cc_final: 0.7907 (mt) REVERT: C 543 THR cc_start: 0.8176 (m) cc_final: 0.7965 (p) REVERT: C 631 LEU cc_start: 0.8481 (mt) cc_final: 0.8254 (mt) REVERT: C 698 ILE cc_start: 0.8504 (mt) cc_final: 0.8251 (mt) REVERT: C 731 ASN cc_start: 0.6335 (t0) cc_final: 0.5997 (t0) REVERT: C 809 THR cc_start: 0.7796 (p) cc_final: 0.7099 (t) REVERT: C 915 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7847 (mmmt) REVERT: C 918 LEU cc_start: 0.7496 (mt) cc_final: 0.7185 (mm) REVERT: C 923 PHE cc_start: 0.7296 (m-10) cc_final: 0.6897 (m-80) REVERT: C 927 TYR cc_start: 0.7121 (m-80) cc_final: 0.6461 (m-80) REVERT: C 940 ILE cc_start: 0.8354 (mm) cc_final: 0.8060 (tp) REVERT: C 948 ILE cc_start: 0.7084 (mm) cc_final: 0.6605 (mm) REVERT: C 949 LYS cc_start: 0.7113 (ttmm) cc_final: 0.6910 (ttmm) REVERT: C 951 LEU cc_start: 0.7815 (mm) cc_final: 0.7562 (mt) REVERT: C 989 GLN cc_start: 0.7434 (tt0) cc_final: 0.6328 (tt0) REVERT: C 999 MET cc_start: 0.7114 (mmm) cc_final: 0.6594 (mmm) REVERT: C 1009 ILE cc_start: 0.7849 (tp) cc_final: 0.7076 (tp) REVERT: C 1013 PHE cc_start: 0.6723 (m-80) cc_final: 0.6204 (m-80) REVERT: C 1035 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6649 (mm-40) REVERT: C 1039 ASN cc_start: 0.6649 (m-40) cc_final: 0.6396 (m-40) REVERT: C 1049 LEU cc_start: 0.8180 (tp) cc_final: 0.7953 (tt) REVERT: C 1083 ILE cc_start: 0.7785 (mt) cc_final: 0.7439 (mm) REVERT: C 1124 SER cc_start: 0.7507 (p) cc_final: 0.7168 (p) REVERT: C 1157 LYS cc_start: 0.7508 (mmmt) cc_final: 0.7075 (mmmt) REVERT: C 1210 MET cc_start: 0.5904 (tpt) cc_final: 0.5610 (mmm) REVERT: A 28 ASP cc_start: 0.7637 (t0) cc_final: 0.7365 (t0) REVERT: A 41 VAL cc_start: 0.8279 (t) cc_final: 0.7711 (p) REVERT: A 108 LYS cc_start: 0.8011 (tttt) cc_final: 0.7715 (tttt) REVERT: A 274 TYR cc_start: 0.7525 (m-10) cc_final: 0.6879 (m-10) REVERT: A 279 ASN cc_start: 0.7428 (p0) cc_final: 0.7134 (p0) REVERT: A 301 LYS cc_start: 0.8158 (tppt) cc_final: 0.7915 (tptm) REVERT: A 313 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 318 THR cc_start: 0.7623 (m) cc_final: 0.7068 (t) REVERT: A 346 VAL cc_start: 0.7995 (p) cc_final: 0.7779 (m) REVERT: A 359 ASN cc_start: 0.7852 (m-40) cc_final: 0.7422 (m-40) REVERT: A 382 ASP cc_start: 0.7321 (p0) cc_final: 0.7070 (p0) REVERT: A 398 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7569 (ttpp) REVERT: A 401 ILE cc_start: 0.8306 (mm) cc_final: 0.8043 (mt) REVERT: A 448 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7576 (m110) REVERT: A 635 ILE cc_start: 0.7878 (mt) cc_final: 0.7596 (pt) REVERT: A 644 TYR cc_start: 0.7036 (m-80) cc_final: 0.6617 (m-80) REVERT: A 671 MET cc_start: 0.7247 (mmm) cc_final: 0.6936 (mmm) REVERT: A 838 SER cc_start: 0.7908 (t) cc_final: 0.7455 (t) REVERT: A 942 VAL cc_start: 0.8315 (p) cc_final: 0.7956 (t) REVERT: A 949 LYS cc_start: 0.7469 (ttmm) cc_final: 0.7235 (ttmm) REVERT: A 999 MET cc_start: 0.6448 (ttp) cc_final: 0.6085 (ttp) REVERT: A 1035 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6804 (tp40) REVERT: A 1098 LEU cc_start: 0.8060 (mp) cc_final: 0.7849 (tp) outliers start: 98 outliers final: 60 residues processed: 1041 average time/residue: 0.4692 time to fit residues: 769.4636 Evaluate side-chains 1021 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 957 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1205 ASN Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 843 ILE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 374 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 380 optimal weight: 2.9990 chunk 403 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 361 ASN B 802 ASN ** B1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 248 HIS C 573 GLN C 649 ASN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1127 ASN H 60 ASN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 303 GLN A 573 GLN A 585 GLN A 590 ASN A 731 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN A1127 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 33690 Z= 0.377 Angle : 0.663 11.419 45870 Z= 0.360 Chirality : 0.049 0.760 5196 Planarity : 0.005 0.052 5889 Dihedral : 6.034 88.279 4887 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.71 % Allowed : 17.64 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4170 helix: 0.46 (0.18), residues: 795 sheet: -0.33 (0.15), residues: 1089 loop : -1.14 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 35 HIS 0.009 0.001 HIS B1134 PHE 0.025 0.002 PHE C 456 TYR 0.027 0.002 TYR C1147 ARG 0.010 0.001 ARG B1055 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1002 time to evaluate : 3.472 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: D 89 GLN cc_start: 0.5725 (OUTLIER) cc_final: 0.5525 (tm-30) REVERT: B 16 ILE cc_start: 0.8122 (mm) cc_final: 0.7918 (mt) REVERT: B 108 LYS cc_start: 0.7958 (tttt) cc_final: 0.7645 (tttt) REVERT: B 206 ASP cc_start: 0.7000 (t0) cc_final: 0.6752 (t70) REVERT: B 262 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7943 (mt) REVERT: B 280 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6751 (mm-40) REVERT: B 299 LYS cc_start: 0.8000 (mttt) cc_final: 0.7507 (mttt) REVERT: B 318 THR cc_start: 0.7482 (m) cc_final: 0.7009 (t) REVERT: B 363 ASN cc_start: 0.5097 (OUTLIER) cc_final: 0.3135 (p0) REVERT: B 398 LYS cc_start: 0.8267 (ttpt) cc_final: 0.8013 (ttpp) REVERT: B 478 VAL cc_start: 0.8293 (p) cc_final: 0.8066 (m) REVERT: B 635 ILE cc_start: 0.8141 (mp) cc_final: 0.7790 (pt) REVERT: B 661 PHE cc_start: 0.7818 (p90) cc_final: 0.7449 (p90) REVERT: B 673 ARG cc_start: 0.7067 (mtp85) cc_final: 0.6708 (ttm110) REVERT: B 768 PHE cc_start: 0.7840 (t80) cc_final: 0.7613 (t80) REVERT: B 866 MET cc_start: 0.6418 (tpp) cc_final: 0.5917 (mpp) REVERT: B 882 ASN cc_start: 0.7853 (t0) cc_final: 0.7597 (t0) REVERT: B 963 TYR cc_start: 0.6756 (m-10) cc_final: 0.6462 (m-10) REVERT: B 995 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7595 (mm) REVERT: B 1035 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6672 (mm-40) REVERT: B 1049 LEU cc_start: 0.8284 (tp) cc_final: 0.8054 (tt) REVERT: B 1134 HIS cc_start: 0.6698 (t-170) cc_final: 0.6367 (t-170) REVERT: B 1187 ASN cc_start: 0.7813 (m-40) cc_final: 0.7422 (t0) REVERT: X 109 TYR cc_start: 0.7180 (t80) cc_final: 0.6739 (t80) REVERT: C 24 ASP cc_start: 0.7428 (t0) cc_final: 0.7108 (t0) REVERT: C 41 VAL cc_start: 0.8221 (t) cc_final: 0.7804 (p) REVERT: C 88 ARG cc_start: 0.7272 (mtt90) cc_final: 0.7047 (mtt90) REVERT: C 119 TYR cc_start: 0.6625 (m-80) cc_final: 0.6416 (m-80) REVERT: C 187 LEU cc_start: 0.7661 (tp) cc_final: 0.7220 (tt) REVERT: C 200 LYS cc_start: 0.6496 (mppt) cc_final: 0.6216 (mptt) REVERT: C 279 ASN cc_start: 0.7492 (p0) cc_final: 0.7167 (p0) REVERT: C 344 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8129 (ptpp) REVERT: C 363 ASN cc_start: 0.5011 (OUTLIER) cc_final: 0.3514 (p0) REVERT: C 382 ASP cc_start: 0.7492 (p0) cc_final: 0.7241 (p0) REVERT: C 433 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7720 (tp) REVERT: C 437 LEU cc_start: 0.8276 (mt) cc_final: 0.7959 (mt) REVERT: C 543 THR cc_start: 0.8243 (m) cc_final: 0.8012 (p) REVERT: C 631 LEU cc_start: 0.8512 (mt) cc_final: 0.8253 (mt) REVERT: C 698 ILE cc_start: 0.8636 (mt) cc_final: 0.8409 (mt) REVERT: C 731 ASN cc_start: 0.6445 (t0) cc_final: 0.6154 (t0) REVERT: C 809 THR cc_start: 0.7720 (p) cc_final: 0.7109 (t) REVERT: C 915 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7978 (mmmt) REVERT: C 927 TYR cc_start: 0.7391 (m-80) cc_final: 0.6997 (m-80) REVERT: C 940 ILE cc_start: 0.8481 (mm) cc_final: 0.8111 (tt) REVERT: C 948 ILE cc_start: 0.7251 (mm) cc_final: 0.6615 (mm) REVERT: C 951 LEU cc_start: 0.7857 (mm) cc_final: 0.7592 (mt) REVERT: C 989 GLN cc_start: 0.7503 (tt0) cc_final: 0.6375 (tt0) REVERT: C 999 MET cc_start: 0.7294 (mmm) cc_final: 0.6621 (mmm) REVERT: C 1009 ILE cc_start: 0.7937 (tp) cc_final: 0.7270 (tp) REVERT: C 1013 PHE cc_start: 0.6890 (m-80) cc_final: 0.6341 (m-80) REVERT: C 1035 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6759 (mm-40) REVERT: C 1049 LEU cc_start: 0.8344 (tp) cc_final: 0.8129 (tt) REVERT: C 1083 ILE cc_start: 0.7849 (mt) cc_final: 0.7576 (mm) REVERT: C 1124 SER cc_start: 0.7335 (p) cc_final: 0.7059 (p) REVERT: C 1157 LYS cc_start: 0.7611 (mmmt) cc_final: 0.7180 (mmmt) REVERT: A 28 ASP cc_start: 0.7664 (t0) cc_final: 0.7430 (t0) REVERT: A 41 VAL cc_start: 0.8370 (t) cc_final: 0.7836 (p) REVERT: A 43 VAL cc_start: 0.6686 (OUTLIER) cc_final: 0.6380 (t) REVERT: A 47 LEU cc_start: 0.8346 (tp) cc_final: 0.7923 (pp) REVERT: A 108 LYS cc_start: 0.8069 (tttt) cc_final: 0.7729 (tttt) REVERT: A 111 LYS cc_start: 0.7968 (mttt) cc_final: 0.7639 (mttp) REVERT: A 136 TYR cc_start: 0.7263 (m-80) cc_final: 0.7024 (m-80) REVERT: A 274 TYR cc_start: 0.7429 (m-10) cc_final: 0.7095 (m-10) REVERT: A 279 ASN cc_start: 0.7625 (p0) cc_final: 0.7215 (p0) REVERT: A 280 GLN cc_start: 0.6759 (tp40) cc_final: 0.6548 (tp-100) REVERT: A 313 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6695 (mm-30) REVERT: A 346 VAL cc_start: 0.8071 (p) cc_final: 0.7838 (m) REVERT: A 359 ASN cc_start: 0.7904 (m-40) cc_final: 0.7528 (m-40) REVERT: A 363 ASN cc_start: 0.5069 (OUTLIER) cc_final: 0.3535 (p0) REVERT: A 398 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7555 (ttpp) REVERT: A 401 ILE cc_start: 0.8421 (mm) cc_final: 0.8186 (mt) REVERT: A 420 PHE cc_start: 0.7685 (m-10) cc_final: 0.7303 (m-10) REVERT: A 612 LYS cc_start: 0.7812 (ptpp) cc_final: 0.7440 (ptpp) REVERT: A 635 ILE cc_start: 0.7945 (mt) cc_final: 0.7698 (pt) REVERT: A 644 TYR cc_start: 0.7160 (m-80) cc_final: 0.6728 (m-80) REVERT: A 649 ASN cc_start: 0.7794 (m-40) cc_final: 0.7568 (m-40) REVERT: A 671 MET cc_start: 0.7066 (mmm) cc_final: 0.6707 (mmm) REVERT: A 865 LEU cc_start: 0.8099 (mt) cc_final: 0.7876 (mt) REVERT: A 866 MET cc_start: 0.6148 (tpp) cc_final: 0.5925 (mpp) REVERT: A 927 TYR cc_start: 0.7387 (m-80) cc_final: 0.7164 (m-80) REVERT: A 940 ILE cc_start: 0.8506 (mm) cc_final: 0.8274 (tp) REVERT: A 942 VAL cc_start: 0.8357 (p) cc_final: 0.8054 (t) REVERT: A 946 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8286 (mmtm) REVERT: A 949 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7401 (ttmm) REVERT: A 963 TYR cc_start: 0.6476 (m-80) cc_final: 0.6138 (m-80) REVERT: A 1191 TYR cc_start: 0.7590 (t80) cc_final: 0.7386 (t80) REVERT: A 1224 MET cc_start: 0.4925 (tpp) cc_final: 0.4686 (tpp) outliers start: 135 outliers final: 85 residues processed: 1063 average time/residue: 0.4545 time to fit residues: 768.4600 Evaluate side-chains 1045 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 952 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1205 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 836 TYR Chi-restraints excluded: chain C residue 843 ILE Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 335 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 0.4980 chunk 343 optimal weight: 0.6980 chunk 278 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 361 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN B 802 ASN ** B1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 573 GLN C 858 GLN ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 731 ASN A 867 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33690 Z= 0.245 Angle : 0.614 10.715 45870 Z= 0.328 Chirality : 0.048 0.914 5196 Planarity : 0.004 0.056 5889 Dihedral : 5.619 80.968 4887 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.71 % Allowed : 18.93 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4170 helix: 0.76 (0.19), residues: 777 sheet: -0.24 (0.16), residues: 1071 loop : -1.14 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 35 HIS 0.008 0.001 HIS B1134 PHE 0.033 0.002 PHE C 285 TYR 0.025 0.002 TYR A 702 ARG 0.013 0.001 ARG A1055 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 961 time to evaluate : 3.814 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: symmetry clash REVERT: B 28 ASP cc_start: 0.6940 (t0) cc_final: 0.6717 (t0) REVERT: B 108 LYS cc_start: 0.7895 (tttt) cc_final: 0.7623 (tttt) REVERT: B 206 ASP cc_start: 0.6858 (t0) cc_final: 0.6641 (t70) REVERT: B 261 THR cc_start: 0.7657 (m) cc_final: 0.7314 (m) REVERT: B 262 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7995 (mt) REVERT: B 318 THR cc_start: 0.7468 (m) cc_final: 0.6928 (t) REVERT: B 363 ASN cc_start: 0.4793 (OUTLIER) cc_final: 0.3324 (p0) REVERT: B 379 ASN cc_start: 0.7170 (t0) cc_final: 0.6958 (t0) REVERT: B 437 LEU cc_start: 0.8341 (mm) cc_final: 0.8063 (mp) REVERT: B 447 PHE cc_start: 0.6469 (m-10) cc_final: 0.6224 (m-10) REVERT: B 619 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7389 (tt) REVERT: B 635 ILE cc_start: 0.8142 (mp) cc_final: 0.7813 (pt) REVERT: B 661 PHE cc_start: 0.7765 (p90) cc_final: 0.7343 (p90) REVERT: B 673 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6711 (ttm110) REVERT: B 714 GLN cc_start: 0.7638 (tp40) cc_final: 0.7217 (tm-30) REVERT: B 731 ASN cc_start: 0.6249 (t0) cc_final: 0.5795 (t0) REVERT: B 768 PHE cc_start: 0.7782 (t80) cc_final: 0.7547 (t80) REVERT: B 865 LEU cc_start: 0.8378 (mt) cc_final: 0.8046 (mt) REVERT: B 866 MET cc_start: 0.6406 (tpp) cc_final: 0.5738 (mpp) REVERT: B 882 ASN cc_start: 0.7811 (t0) cc_final: 0.7567 (t0) REVERT: B 918 LEU cc_start: 0.7346 (mt) cc_final: 0.7064 (mp) REVERT: B 943 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.6088 (mt0) REVERT: B 963 TYR cc_start: 0.6680 (m-10) cc_final: 0.6301 (m-10) REVERT: B 995 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7443 (mm) REVERT: B 1035 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6677 (mm-40) REVERT: B 1039 ASN cc_start: 0.6394 (m-40) cc_final: 0.6151 (m110) REVERT: B 1049 LEU cc_start: 0.8276 (tp) cc_final: 0.8030 (tt) REVERT: B 1187 ASN cc_start: 0.7759 (m-40) cc_final: 0.7331 (t0) REVERT: X 109 TYR cc_start: 0.7166 (t80) cc_final: 0.6783 (t80) REVERT: C 24 ASP cc_start: 0.7377 (t0) cc_final: 0.7081 (t0) REVERT: C 41 VAL cc_start: 0.8263 (t) cc_final: 0.7834 (p) REVERT: C 119 TYR cc_start: 0.6507 (m-80) cc_final: 0.6300 (m-80) REVERT: C 200 LYS cc_start: 0.6369 (mppt) cc_final: 0.6101 (mptt) REVERT: C 279 ASN cc_start: 0.7401 (p0) cc_final: 0.7177 (p0) REVERT: C 344 LYS cc_start: 0.8486 (ptpt) cc_final: 0.8127 (ptpp) REVERT: C 363 ASN cc_start: 0.4848 (OUTLIER) cc_final: 0.3304 (p0) REVERT: C 437 LEU cc_start: 0.8251 (mt) cc_final: 0.7967 (mt) REVERT: C 455 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7029 (ptm-80) REVERT: C 635 ILE cc_start: 0.7979 (mp) cc_final: 0.7623 (pt) REVERT: C 684 PHE cc_start: 0.7444 (t80) cc_final: 0.6959 (t80) REVERT: C 698 ILE cc_start: 0.8678 (mt) cc_final: 0.8334 (mt) REVERT: C 731 ASN cc_start: 0.6302 (t0) cc_final: 0.6021 (t0) REVERT: C 927 TYR cc_start: 0.7285 (m-80) cc_final: 0.6972 (m-80) REVERT: C 940 ILE cc_start: 0.8306 (mm) cc_final: 0.8105 (tt) REVERT: C 948 ILE cc_start: 0.7166 (mm) cc_final: 0.6631 (mm) REVERT: C 951 LEU cc_start: 0.7861 (mm) cc_final: 0.7627 (mt) REVERT: C 989 GLN cc_start: 0.7464 (tt0) cc_final: 0.6881 (tt0) REVERT: C 999 MET cc_start: 0.7286 (mmm) cc_final: 0.6430 (mmm) REVERT: C 1009 ILE cc_start: 0.7895 (tp) cc_final: 0.7262 (tp) REVERT: C 1013 PHE cc_start: 0.6792 (m-80) cc_final: 0.6225 (m-80) REVERT: C 1035 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6810 (mm-40) REVERT: C 1039 ASN cc_start: 0.6640 (m-40) cc_final: 0.6350 (m-40) REVERT: C 1049 LEU cc_start: 0.8299 (tp) cc_final: 0.8089 (tt) REVERT: C 1083 ILE cc_start: 0.7850 (mt) cc_final: 0.7213 (mm) REVERT: C 1087 LEU cc_start: 0.7453 (mm) cc_final: 0.7164 (mm) REVERT: C 1124 SER cc_start: 0.7439 (p) cc_final: 0.7129 (p) REVERT: C 1157 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7165 (mmmt) REVERT: C 1210 MET cc_start: 0.6306 (tpt) cc_final: 0.5829 (mmm) REVERT: A 28 ASP cc_start: 0.7562 (t0) cc_final: 0.7323 (t0) REVERT: A 43 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6426 (t) REVERT: A 47 LEU cc_start: 0.8349 (tp) cc_final: 0.7967 (pp) REVERT: A 108 LYS cc_start: 0.8045 (tttt) cc_final: 0.7729 (tttt) REVERT: A 111 LYS cc_start: 0.7894 (mttt) cc_final: 0.7576 (mttp) REVERT: A 136 TYR cc_start: 0.7295 (m-80) cc_final: 0.7090 (m-80) REVERT: A 274 TYR cc_start: 0.7267 (m-10) cc_final: 0.7028 (m-10) REVERT: A 279 ASN cc_start: 0.7506 (p0) cc_final: 0.7272 (p0) REVERT: A 280 GLN cc_start: 0.6797 (tp40) cc_final: 0.6586 (tp-100) REVERT: A 346 VAL cc_start: 0.8028 (p) cc_final: 0.7806 (m) REVERT: A 359 ASN cc_start: 0.7893 (m-40) cc_final: 0.7577 (m-40) REVERT: A 363 ASN cc_start: 0.5080 (OUTLIER) cc_final: 0.3484 (p0) REVERT: A 398 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7548 (ttpp) REVERT: A 401 ILE cc_start: 0.8388 (mm) cc_final: 0.8142 (mt) REVERT: A 573 GLN cc_start: 0.7424 (mm110) cc_final: 0.7065 (mp10) REVERT: A 612 LYS cc_start: 0.7798 (ptpp) cc_final: 0.7489 (ptpp) REVERT: A 644 TYR cc_start: 0.7034 (m-80) cc_final: 0.6675 (m-80) REVERT: A 649 ASN cc_start: 0.7812 (m-40) cc_final: 0.7504 (m-40) REVERT: A 671 MET cc_start: 0.7153 (mmm) cc_final: 0.6876 (mmm) REVERT: A 865 LEU cc_start: 0.8094 (mt) cc_final: 0.7747 (mt) REVERT: A 866 MET cc_start: 0.6261 (tpp) cc_final: 0.5908 (mpp) REVERT: A 927 TYR cc_start: 0.7294 (m-80) cc_final: 0.6903 (m-80) REVERT: A 940 ILE cc_start: 0.8486 (mm) cc_final: 0.7986 (tt) REVERT: A 942 VAL cc_start: 0.8403 (p) cc_final: 0.7934 (t) REVERT: A 946 LYS cc_start: 0.8527 (mmtm) cc_final: 0.8217 (mmtm) REVERT: A 963 TYR cc_start: 0.6465 (m-80) cc_final: 0.6081 (m-80) REVERT: A 1055 ARG cc_start: 0.7023 (mtm110) cc_final: 0.6737 (mtm110) REVERT: A 1224 MET cc_start: 0.4883 (tpp) cc_final: 0.4682 (tpp) outliers start: 135 outliers final: 84 residues processed: 1018 average time/residue: 0.4697 time to fit residues: 762.4646 Evaluate side-chains 1038 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 945 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain X residue 7 TRP Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 455 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 135 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 403 optimal weight: 0.9980 chunk 334 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 280 GLN B 380 ASN B 590 ASN B 655 ASN B 802 ASN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN ** B1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN C 248 HIS C 573 GLN C 738 GLN C 858 GLN ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN H 60 ASN ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS A 655 ASN A 731 ASN A 851 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 33690 Z= 0.212 Angle : 0.605 12.683 45870 Z= 0.321 Chirality : 0.047 0.797 5196 Planarity : 0.004 0.054 5889 Dihedral : 5.336 70.762 4887 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.82 % Allowed : 19.32 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4170 helix: 0.91 (0.19), residues: 774 sheet: -0.16 (0.16), residues: 1050 loop : -1.09 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 35 HIS 0.016 0.001 HIS C1134 PHE 0.027 0.002 PHE C 285 TYR 0.026 0.002 TYR C 963 ARG 0.011 0.001 ARG B1055 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 958 time to evaluate : 3.697 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: B 108 LYS cc_start: 0.7899 (tttt) cc_final: 0.7626 (tttt) REVERT: B 206 ASP cc_start: 0.6847 (t0) cc_final: 0.6627 (t70) REVERT: B 213 TYR cc_start: 0.7804 (m-10) cc_final: 0.7548 (m-10) REVERT: B 261 THR cc_start: 0.7684 (m) cc_final: 0.7333 (m) REVERT: B 363 ASN cc_start: 0.4662 (OUTLIER) cc_final: 0.2690 (p0) REVERT: B 379 ASN cc_start: 0.7205 (t0) cc_final: 0.6993 (t0) REVERT: B 437 LEU cc_start: 0.8317 (mm) cc_final: 0.8049 (mp) REVERT: B 447 PHE cc_start: 0.6488 (m-10) cc_final: 0.6259 (m-10) REVERT: B 619 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7387 (tt) REVERT: B 635 ILE cc_start: 0.8089 (mp) cc_final: 0.7651 (pt) REVERT: B 673 ARG cc_start: 0.7067 (mtp85) cc_final: 0.6708 (ttm110) REVERT: B 714 GLN cc_start: 0.7632 (tp40) cc_final: 0.7235 (tm-30) REVERT: B 835 GLU cc_start: 0.5861 (mm-30) cc_final: 0.5354 (mm-30) REVERT: B 865 LEU cc_start: 0.8373 (mt) cc_final: 0.8099 (mt) REVERT: B 866 MET cc_start: 0.6216 (tpp) cc_final: 0.5703 (mpp) REVERT: B 874 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8068 (mmtt) REVERT: B 882 ASN cc_start: 0.7823 (t0) cc_final: 0.7423 (t0) REVERT: B 943 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.6027 (mt0) REVERT: B 963 TYR cc_start: 0.6625 (m-10) cc_final: 0.6254 (m-10) REVERT: B 995 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7441 (mm) REVERT: B 1035 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6486 (mm-40) REVERT: B 1049 LEU cc_start: 0.8263 (tp) cc_final: 0.8004 (tt) REVERT: B 1114 LYS cc_start: 0.7220 (tttm) cc_final: 0.6788 (ttmt) REVERT: B 1134 HIS cc_start: 0.6353 (t-170) cc_final: 0.5848 (t-170) REVERT: B 1150 HIS cc_start: 0.7241 (m90) cc_final: 0.6963 (m-70) REVERT: B 1187 ASN cc_start: 0.7712 (m-40) cc_final: 0.7312 (t0) REVERT: X 109 TYR cc_start: 0.7202 (t80) cc_final: 0.6817 (t80) REVERT: F 89 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.5746 (tm-30) REVERT: C 24 ASP cc_start: 0.7299 (t0) cc_final: 0.7022 (t0) REVERT: C 88 ARG cc_start: 0.7258 (mtt90) cc_final: 0.7056 (mtt90) REVERT: C 108 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7509 (tmtt) REVERT: C 279 ASN cc_start: 0.7347 (p0) cc_final: 0.6911 (p0) REVERT: C 344 LYS cc_start: 0.8427 (ptpt) cc_final: 0.8098 (ptpp) REVERT: C 363 ASN cc_start: 0.4461 (OUTLIER) cc_final: 0.3258 (p0) REVERT: C 437 LEU cc_start: 0.8249 (mt) cc_final: 0.7959 (mt) REVERT: C 635 ILE cc_start: 0.7944 (mp) cc_final: 0.7622 (pt) REVERT: C 670 PHE cc_start: 0.8204 (m-80) cc_final: 0.7890 (m-80) REVERT: C 698 ILE cc_start: 0.8703 (mt) cc_final: 0.8402 (mt) REVERT: C 731 ASN cc_start: 0.6213 (t0) cc_final: 0.5921 (t0) REVERT: C 927 TYR cc_start: 0.7264 (m-80) cc_final: 0.7022 (m-80) REVERT: C 942 VAL cc_start: 0.8353 (p) cc_final: 0.8062 (t) REVERT: C 948 ILE cc_start: 0.7195 (mm) cc_final: 0.6616 (mm) REVERT: C 989 GLN cc_start: 0.7473 (tt0) cc_final: 0.6864 (tt0) REVERT: C 999 MET cc_start: 0.7219 (mmm) cc_final: 0.6303 (mmm) REVERT: C 1009 ILE cc_start: 0.7949 (tp) cc_final: 0.7317 (tp) REVERT: C 1013 PHE cc_start: 0.6769 (m-80) cc_final: 0.6190 (m-80) REVERT: C 1035 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6633 (mm-40) REVERT: C 1049 LEU cc_start: 0.8300 (tp) cc_final: 0.8070 (tt) REVERT: C 1069 ARG cc_start: 0.7010 (mtp180) cc_final: 0.6803 (ptm160) REVERT: C 1082 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7791 (mm) REVERT: C 1083 ILE cc_start: 0.7811 (mt) cc_final: 0.7515 (mm) REVERT: C 1087 LEU cc_start: 0.7466 (mm) cc_final: 0.7225 (mt) REVERT: C 1124 SER cc_start: 0.7365 (p) cc_final: 0.7120 (p) REVERT: C 1134 HIS cc_start: 0.6720 (t-170) cc_final: 0.6175 (t-170) REVERT: C 1157 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7163 (mmmt) REVERT: A 28 ASP cc_start: 0.7538 (t0) cc_final: 0.7258 (t0) REVERT: A 47 LEU cc_start: 0.8322 (tp) cc_final: 0.7923 (pp) REVERT: A 108 LYS cc_start: 0.8027 (tttt) cc_final: 0.7713 (tttt) REVERT: A 111 LYS cc_start: 0.7905 (mttt) cc_final: 0.7498 (mttp) REVERT: A 279 ASN cc_start: 0.7437 (p0) cc_final: 0.7222 (p0) REVERT: A 346 VAL cc_start: 0.8006 (p) cc_final: 0.7696 (m) REVERT: A 359 ASN cc_start: 0.7857 (m-40) cc_final: 0.7462 (m-40) REVERT: A 363 ASN cc_start: 0.5189 (OUTLIER) cc_final: 0.4100 (p0) REVERT: A 364 MET cc_start: 0.5732 (tmm) cc_final: 0.5476 (tmm) REVERT: A 382 ASP cc_start: 0.7192 (p0) cc_final: 0.6289 (m-30) REVERT: A 398 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7514 (ttpp) REVERT: A 401 ILE cc_start: 0.8359 (mm) cc_final: 0.8135 (mt) REVERT: A 644 TYR cc_start: 0.7027 (m-80) cc_final: 0.6700 (m-80) REVERT: A 649 ASN cc_start: 0.7801 (m-40) cc_final: 0.7535 (t0) REVERT: A 671 MET cc_start: 0.7127 (mmm) cc_final: 0.6816 (mmm) REVERT: A 699 LYS cc_start: 0.7458 (mmtp) cc_final: 0.7026 (mttp) REVERT: A 865 LEU cc_start: 0.8134 (mt) cc_final: 0.7797 (mt) REVERT: A 866 MET cc_start: 0.6201 (tpp) cc_final: 0.5882 (mpp) REVERT: A 940 ILE cc_start: 0.8448 (mm) cc_final: 0.8068 (tt) REVERT: A 942 VAL cc_start: 0.8254 (p) cc_final: 0.7841 (t) REVERT: A 963 TYR cc_start: 0.6457 (m-80) cc_final: 0.6002 (m-80) REVERT: A 1120 LYS cc_start: 0.7227 (mttt) cc_final: 0.6833 (mmtt) REVERT: A 1125 ARG cc_start: 0.7183 (mmm-85) cc_final: 0.6754 (mtp180) REVERT: A 1128 PHE cc_start: 0.7291 (t80) cc_final: 0.6788 (t80) REVERT: A 1224 MET cc_start: 0.4878 (tpp) cc_final: 0.4672 (tpp) outliers start: 139 outliers final: 102 residues processed: 1016 average time/residue: 0.4633 time to fit residues: 752.5086 Evaluate side-chains 1061 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 951 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 7 TRP Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1224 MET Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 388 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 228 optimal weight: 0.0030 chunk 339 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 401 optimal weight: 0.8980 chunk 251 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 361 ASN B 453 ASN B 738 GLN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS C 573 GLN ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN A 248 HIS ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33690 Z= 0.190 Angle : 0.613 13.364 45870 Z= 0.322 Chirality : 0.046 0.746 5196 Planarity : 0.004 0.054 5889 Dihedral : 5.084 55.071 4887 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.52 % Allowed : 20.64 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4170 helix: 1.09 (0.19), residues: 765 sheet: -0.08 (0.16), residues: 1050 loop : -1.07 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 35 HIS 0.014 0.001 HIS C1134 PHE 0.024 0.001 PHE A 420 TYR 0.024 0.001 TYR C 702 ARG 0.012 0.001 ARG B1055 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 947 time to evaluate : 3.615 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: B 108 LYS cc_start: 0.7884 (tttt) cc_final: 0.7610 (tttt) REVERT: B 206 ASP cc_start: 0.6810 (t0) cc_final: 0.6589 (t70) REVERT: B 213 TYR cc_start: 0.7800 (m-10) cc_final: 0.7519 (m-10) REVERT: B 261 THR cc_start: 0.7648 (m) cc_final: 0.7344 (m) REVERT: B 363 ASN cc_start: 0.4675 (OUTLIER) cc_final: 0.3175 (p0) REVERT: B 437 LEU cc_start: 0.8337 (mm) cc_final: 0.8027 (mp) REVERT: B 447 PHE cc_start: 0.6465 (m-10) cc_final: 0.6226 (m-10) REVERT: B 635 ILE cc_start: 0.7956 (mp) cc_final: 0.7569 (pt) REVERT: B 673 ARG cc_start: 0.7063 (mtp85) cc_final: 0.6680 (ttm110) REVERT: B 714 GLN cc_start: 0.7611 (tp40) cc_final: 0.7263 (tm-30) REVERT: B 866 MET cc_start: 0.6290 (tpp) cc_final: 0.5753 (mpp) REVERT: B 874 LYS cc_start: 0.8282 (mmtt) cc_final: 0.8081 (mmtt) REVERT: B 882 ASN cc_start: 0.7780 (t0) cc_final: 0.7443 (t0) REVERT: B 918 LEU cc_start: 0.7251 (mt) cc_final: 0.6773 (mp) REVERT: B 943 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.6070 (mt0) REVERT: B 963 TYR cc_start: 0.6572 (m-10) cc_final: 0.6249 (m-10) REVERT: B 995 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7378 (mm) REVERT: B 1035 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6726 (mm-40) REVERT: B 1049 LEU cc_start: 0.8236 (tp) cc_final: 0.7981 (tt) REVERT: B 1134 HIS cc_start: 0.6355 (t-170) cc_final: 0.6077 (t-170) REVERT: B 1150 HIS cc_start: 0.7245 (m90) cc_final: 0.6859 (m-70) REVERT: B 1187 ASN cc_start: 0.7712 (m-40) cc_final: 0.7309 (t0) REVERT: X 109 TYR cc_start: 0.7160 (t80) cc_final: 0.6757 (t80) REVERT: C 24 ASP cc_start: 0.7311 (t0) cc_final: 0.7029 (t0) REVERT: C 88 ARG cc_start: 0.7256 (mtt90) cc_final: 0.7027 (mtt90) REVERT: C 108 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7456 (tmtt) REVERT: C 295 MET cc_start: 0.5836 (tpt) cc_final: 0.5504 (tpt) REVERT: C 299 LYS cc_start: 0.7720 (mttt) cc_final: 0.7362 (mttm) REVERT: C 301 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7887 (ttpp) REVERT: C 344 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8037 (ptpp) REVERT: C 363 ASN cc_start: 0.4437 (OUTLIER) cc_final: 0.3260 (p0) REVERT: C 382 ASP cc_start: 0.7740 (p0) cc_final: 0.7515 (p0) REVERT: C 437 LEU cc_start: 0.8255 (mt) cc_final: 0.7951 (mt) REVERT: C 488 LYS cc_start: 0.7961 (tppt) cc_final: 0.7693 (tppt) REVERT: C 635 ILE cc_start: 0.7945 (mp) cc_final: 0.7606 (pt) REVERT: C 670 PHE cc_start: 0.8138 (m-80) cc_final: 0.7808 (m-80) REVERT: C 698 ILE cc_start: 0.8597 (mt) cc_final: 0.8274 (mt) REVERT: C 731 ASN cc_start: 0.6143 (t0) cc_final: 0.5815 (t0) REVERT: C 738 GLN cc_start: 0.7460 (mm-40) cc_final: 0.7184 (mm110) REVERT: C 809 THR cc_start: 0.7589 (p) cc_final: 0.7037 (t) REVERT: C 927 TYR cc_start: 0.7238 (m-80) cc_final: 0.7022 (m-80) REVERT: C 989 GLN cc_start: 0.7502 (tt0) cc_final: 0.6726 (tt0) REVERT: C 999 MET cc_start: 0.7239 (mmm) cc_final: 0.6200 (mmm) REVERT: C 1009 ILE cc_start: 0.7934 (tp) cc_final: 0.7234 (tp) REVERT: C 1013 PHE cc_start: 0.6723 (m-80) cc_final: 0.6174 (m-80) REVERT: C 1035 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6830 (mm-40) REVERT: C 1049 LEU cc_start: 0.8311 (tp) cc_final: 0.8088 (tt) REVERT: C 1069 ARG cc_start: 0.6965 (mtp180) cc_final: 0.6706 (ptm160) REVERT: C 1083 ILE cc_start: 0.7848 (mt) cc_final: 0.7517 (mm) REVERT: C 1087 LEU cc_start: 0.7449 (mm) cc_final: 0.7234 (mt) REVERT: C 1124 SER cc_start: 0.7345 (p) cc_final: 0.7066 (p) REVERT: C 1157 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7159 (mmmt) REVERT: A 28 ASP cc_start: 0.7466 (t0) cc_final: 0.7225 (t0) REVERT: A 47 LEU cc_start: 0.8316 (tp) cc_final: 0.7981 (pp) REVERT: A 108 LYS cc_start: 0.8012 (tttt) cc_final: 0.7719 (tttt) REVERT: A 111 LYS cc_start: 0.7802 (mttt) cc_final: 0.7494 (mttp) REVERT: A 359 ASN cc_start: 0.7808 (m-40) cc_final: 0.7588 (m-40) REVERT: A 363 ASN cc_start: 0.5384 (OUTLIER) cc_final: 0.4231 (p0) REVERT: A 368 MET cc_start: 0.6502 (mtm) cc_final: 0.6234 (mtm) REVERT: A 382 ASP cc_start: 0.7190 (p0) cc_final: 0.6222 (m-30) REVERT: A 401 ILE cc_start: 0.8352 (mm) cc_final: 0.8098 (mt) REVERT: A 644 TYR cc_start: 0.7031 (m-80) cc_final: 0.6711 (m-80) REVERT: A 649 ASN cc_start: 0.7798 (m-40) cc_final: 0.7501 (t0) REVERT: A 671 MET cc_start: 0.7085 (mmm) cc_final: 0.6791 (mmm) REVERT: A 851 ASN cc_start: 0.6971 (m110) cc_final: 0.6765 (m110) REVERT: A 865 LEU cc_start: 0.8151 (mt) cc_final: 0.7705 (mt) REVERT: A 866 MET cc_start: 0.6098 (tpp) cc_final: 0.5721 (mpp) REVERT: A 942 VAL cc_start: 0.8261 (p) cc_final: 0.7949 (t) REVERT: A 963 TYR cc_start: 0.6376 (m-80) cc_final: 0.5987 (m-80) REVERT: A 1120 LYS cc_start: 0.7063 (mttt) cc_final: 0.6776 (mmmm) outliers start: 128 outliers final: 95 residues processed: 995 average time/residue: 0.4458 time to fit residues: 707.8579 Evaluate side-chains 1037 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 937 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1021 GLN Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1224 MET Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1118 CYS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN B 590 ASN B 649 ASN B 655 ASN B 738 GLN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN ** C1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 731 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 33690 Z= 0.465 Angle : 0.736 13.423 45870 Z= 0.398 Chirality : 0.051 0.700 5196 Planarity : 0.005 0.054 5889 Dihedral : 5.608 59.782 4887 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.60 % Allowed : 20.97 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.02 (0.13), residues: 4170 helix: 0.40 (0.18), residues: 792 sheet: -0.23 (0.16), residues: 1032 loop : -1.27 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP D 94 HIS 0.012 0.002 HIS C 177 PHE 0.045 0.003 PHE C 456 TYR 0.031 0.002 TYR A 68 ARG 0.014 0.001 ARG B1055 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 972 time to evaluate : 3.590 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: B 47 LEU cc_start: 0.8188 (tp) cc_final: 0.7824 (pp) REVERT: B 108 LYS cc_start: 0.7907 (tttt) cc_final: 0.7565 (tttt) REVERT: B 206 ASP cc_start: 0.7083 (t0) cc_final: 0.6880 (t70) REVERT: B 213 TYR cc_start: 0.7889 (m-10) cc_final: 0.7533 (m-10) REVERT: B 219 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6311 (mm-30) REVERT: B 259 LYS cc_start: 0.8233 (tppt) cc_final: 0.7969 (tppt) REVERT: B 363 ASN cc_start: 0.4760 (OUTLIER) cc_final: 0.2864 (p0) REVERT: B 418 GLN cc_start: 0.6799 (tt0) cc_final: 0.6553 (tt0) REVERT: B 447 PHE cc_start: 0.6716 (m-10) cc_final: 0.6448 (m-10) REVERT: B 635 ILE cc_start: 0.8144 (mp) cc_final: 0.7825 (pt) REVERT: B 673 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6811 (ttm110) REVERT: B 714 GLN cc_start: 0.7735 (tp40) cc_final: 0.7419 (tm-30) REVERT: B 791 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6679 (mm-30) REVERT: B 865 LEU cc_start: 0.8411 (mt) cc_final: 0.8165 (mt) REVERT: B 866 MET cc_start: 0.6274 (tpp) cc_final: 0.5933 (mpp) REVERT: B 874 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8125 (mmtt) REVERT: B 882 ASN cc_start: 0.7775 (t0) cc_final: 0.7512 (t0) REVERT: B 949 LYS cc_start: 0.7858 (tppp) cc_final: 0.7428 (ttmm) REVERT: B 963 TYR cc_start: 0.6638 (m-10) cc_final: 0.6184 (m-10) REVERT: B 995 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7614 (mm) REVERT: B 1004 GLN cc_start: 0.7849 (pm20) cc_final: 0.7361 (pm20) REVERT: B 1035 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6625 (mm-40) REVERT: B 1049 LEU cc_start: 0.8378 (tp) cc_final: 0.8145 (tt) REVERT: B 1150 HIS cc_start: 0.7140 (m90) cc_final: 0.6867 (m-70) REVERT: B 1157 LYS cc_start: 0.7544 (mmmt) cc_final: 0.7100 (mmmt) REVERT: B 1159 VAL cc_start: 0.8194 (p) cc_final: 0.7963 (t) REVERT: B 1187 ASN cc_start: 0.7791 (m-40) cc_final: 0.7403 (t0) REVERT: X 66 ARG cc_start: 0.6068 (ptm160) cc_final: 0.5767 (tmt170) REVERT: X 109 TYR cc_start: 0.7332 (t80) cc_final: 0.6889 (t80) REVERT: C 24 ASP cc_start: 0.7330 (t0) cc_final: 0.7016 (t0) REVERT: C 88 ARG cc_start: 0.7300 (mtt90) cc_final: 0.7037 (mtt90) REVERT: C 108 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7570 (tmtt) REVERT: C 119 TYR cc_start: 0.6731 (m-80) cc_final: 0.6498 (m-80) REVERT: C 295 MET cc_start: 0.6113 (tpt) cc_final: 0.5578 (tpt) REVERT: C 299 LYS cc_start: 0.7862 (mttt) cc_final: 0.7573 (mttt) REVERT: C 344 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8041 (ptpp) REVERT: C 363 ASN cc_start: 0.5280 (OUTLIER) cc_final: 0.4202 (p0) REVERT: C 414 LEU cc_start: 0.7685 (mp) cc_final: 0.7438 (mt) REVERT: C 437 LEU cc_start: 0.8325 (mt) cc_final: 0.7983 (mt) REVERT: C 670 PHE cc_start: 0.8271 (m-80) cc_final: 0.7985 (m-80) REVERT: C 671 MET cc_start: 0.6884 (mmm) cc_final: 0.6547 (mmm) REVERT: C 698 ILE cc_start: 0.8634 (mt) cc_final: 0.8385 (mt) REVERT: C 746 SER cc_start: 0.8420 (m) cc_final: 0.7825 (t) REVERT: C 806 PHE cc_start: 0.8391 (t80) cc_final: 0.7971 (t80) REVERT: C 927 TYR cc_start: 0.7523 (m-80) cc_final: 0.7029 (m-80) REVERT: C 942 VAL cc_start: 0.8398 (p) cc_final: 0.8140 (t) REVERT: C 948 ILE cc_start: 0.7241 (mm) cc_final: 0.6763 (mm) REVERT: C 989 GLN cc_start: 0.7580 (tt0) cc_final: 0.6782 (tt0) REVERT: C 999 MET cc_start: 0.7298 (mmm) cc_final: 0.6265 (mmm) REVERT: C 1009 ILE cc_start: 0.8052 (tp) cc_final: 0.7355 (tp) REVERT: C 1013 PHE cc_start: 0.6945 (m-80) cc_final: 0.6449 (m-80) REVERT: C 1035 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6981 (mm-40) REVERT: C 1049 LEU cc_start: 0.8424 (tp) cc_final: 0.8219 (tt) REVERT: C 1083 ILE cc_start: 0.7993 (mt) cc_final: 0.7644 (mm) REVERT: C 1124 SER cc_start: 0.7410 (p) cc_final: 0.7069 (p) REVERT: C 1134 HIS cc_start: 0.6777 (t-170) cc_final: 0.6340 (t-170) REVERT: C 1157 LYS cc_start: 0.7570 (mmmt) cc_final: 0.7233 (mmmt) REVERT: A 28 ASP cc_start: 0.7662 (t0) cc_final: 0.7422 (t0) REVERT: A 47 LEU cc_start: 0.8350 (tp) cc_final: 0.8074 (pp) REVERT: A 98 ASP cc_start: 0.7238 (p0) cc_final: 0.6945 (p0) REVERT: A 100 ILE cc_start: 0.8303 (mp) cc_final: 0.8072 (mm) REVERT: A 305 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8009 (mm) REVERT: A 313 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6404 (mm-30) REVERT: A 318 THR cc_start: 0.7679 (m) cc_final: 0.7107 (t) REVERT: A 359 ASN cc_start: 0.7983 (m-40) cc_final: 0.7705 (m-40) REVERT: A 423 ARG cc_start: 0.7701 (tpp-160) cc_final: 0.7432 (tpp80) REVERT: A 447 PHE cc_start: 0.6553 (m-10) cc_final: 0.6291 (m-10) REVERT: A 644 TYR cc_start: 0.7179 (m-80) cc_final: 0.6848 (m-80) REVERT: A 649 ASN cc_start: 0.7780 (m-40) cc_final: 0.7566 (m110) REVERT: A 671 MET cc_start: 0.6996 (mmm) cc_final: 0.6693 (mmm) REVERT: A 847 LEU cc_start: 0.7765 (mt) cc_final: 0.7519 (mt) REVERT: A 865 LEU cc_start: 0.8015 (mt) cc_final: 0.7704 (mt) REVERT: A 942 VAL cc_start: 0.8304 (p) cc_final: 0.8011 (t) REVERT: A 1120 LYS cc_start: 0.7339 (mttt) cc_final: 0.7014 (mmmm) REVERT: A 1136 ILE cc_start: 0.7619 (mm) cc_final: 0.7292 (mm) outliers start: 131 outliers final: 104 residues processed: 1026 average time/residue: 0.4476 time to fit residues: 739.7781 Evaluate side-chains 1062 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 954 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 LEU 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 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1205 ASN Chi-restraints excluded: chain B residue 1224 MET Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 95 CYS Chi-restraints excluded: chain X residue 111 MET Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 365 optimal weight: 0.7980 chunk 385 optimal weight: 0.2980 chunk 351 optimal weight: 0.7980 chunk 374 optimal weight: 0.6980 chunk 384 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 294 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 338 optimal weight: 0.9980 chunk 354 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS C 453 ASN C 573 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 731 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33690 Z= 0.200 Angle : 0.664 12.151 45870 Z= 0.350 Chirality : 0.047 0.687 5196 Planarity : 0.004 0.054 5889 Dihedral : 5.154 51.011 4887 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 3.08 % Allowed : 22.78 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4170 helix: 1.01 (0.19), residues: 744 sheet: -0.16 (0.16), residues: 1035 loop : -1.13 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 94 HIS 0.009 0.001 HIS A 177 PHE 0.034 0.002 PHE C 285 TYR 0.052 0.002 TYR A 274 ARG 0.014 0.001 ARG B1055 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 951 time to evaluate : 3.534 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: B 47 LEU cc_start: 0.8176 (tp) cc_final: 0.7732 (pp) REVERT: B 96 LEU cc_start: 0.8050 (tp) cc_final: 0.7759 (tt) REVERT: B 108 LYS cc_start: 0.7854 (tttt) cc_final: 0.7509 (tttt) REVERT: B 145 ILE cc_start: 0.7739 (pt) cc_final: 0.7531 (mp) REVERT: B 184 ARG cc_start: 0.6477 (mtt180) cc_final: 0.6034 (mmt90) REVERT: B 213 TYR cc_start: 0.7816 (m-10) cc_final: 0.7436 (m-10) REVERT: B 318 THR cc_start: 0.7633 (m) cc_final: 0.7258 (t) REVERT: B 363 ASN cc_start: 0.4852 (OUTLIER) cc_final: 0.3405 (p0) REVERT: B 447 PHE cc_start: 0.6450 (m-10) cc_final: 0.6189 (m-10) REVERT: B 488 LYS cc_start: 0.8254 (tppt) cc_final: 0.7959 (tppt) REVERT: B 635 ILE cc_start: 0.7983 (mp) cc_final: 0.7607 (pt) REVERT: B 673 ARG cc_start: 0.7086 (mtp85) cc_final: 0.6735 (ttm110) REVERT: B 714 GLN cc_start: 0.7659 (tp40) cc_final: 0.7332 (tm-30) REVERT: B 865 LEU cc_start: 0.8330 (mt) cc_final: 0.8051 (mt) REVERT: B 866 MET cc_start: 0.6254 (tpp) cc_final: 0.5692 (mpp) REVERT: B 882 ASN cc_start: 0.7822 (t0) cc_final: 0.7569 (t0) REVERT: B 918 LEU cc_start: 0.7285 (mt) cc_final: 0.7083 (mp) REVERT: B 949 LYS cc_start: 0.7629 (tppp) cc_final: 0.7206 (ttmm) REVERT: B 963 TYR cc_start: 0.6621 (m-10) cc_final: 0.6211 (m-10) REVERT: B 995 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 1049 LEU cc_start: 0.8280 (tp) cc_final: 0.8043 (tt) REVERT: B 1129 CYS cc_start: 0.5357 (t) cc_final: 0.4997 (t) REVERT: B 1134 HIS cc_start: 0.6433 (t-170) cc_final: 0.5738 (t-170) REVERT: B 1150 HIS cc_start: 0.7116 (m90) cc_final: 0.6729 (m-70) REVERT: B 1157 LYS cc_start: 0.7506 (mmmt) cc_final: 0.7039 (mmmt) REVERT: B 1187 ASN cc_start: 0.7719 (m-40) cc_final: 0.7324 (t0) REVERT: X 34 TRP cc_start: 0.7270 (m100) cc_final: 0.6796 (m-10) REVERT: X 66 ARG cc_start: 0.5926 (ptm160) cc_final: 0.5567 (tmt170) REVERT: X 109 TYR cc_start: 0.7270 (t80) cc_final: 0.6827 (t80) REVERT: C 24 ASP cc_start: 0.7310 (t0) cc_final: 0.7011 (t0) REVERT: C 88 ARG cc_start: 0.7318 (mtt90) cc_final: 0.7036 (mtt90) REVERT: C 108 LYS cc_start: 0.7988 (tmtt) cc_final: 0.7452 (tmtt) REVERT: C 344 LYS cc_start: 0.8391 (ptpt) cc_final: 0.7960 (ptpp) REVERT: C 363 ASN cc_start: 0.4588 (OUTLIER) cc_final: 0.3387 (p0) REVERT: C 382 ASP cc_start: 0.7478 (p0) cc_final: 0.7132 (p0) REVERT: C 437 LEU cc_start: 0.8313 (mt) cc_final: 0.7985 (mt) REVERT: C 488 LYS cc_start: 0.7849 (tppt) cc_final: 0.7299 (tppt) REVERT: C 670 PHE cc_start: 0.8147 (m-80) cc_final: 0.7878 (m-80) REVERT: C 671 MET cc_start: 0.6829 (mmm) cc_final: 0.6575 (mmm) REVERT: C 709 LEU cc_start: 0.7685 (mm) cc_final: 0.6980 (mm) REVERT: C 772 GLU cc_start: 0.6581 (tp30) cc_final: 0.6227 (tp30) REVERT: C 809 THR cc_start: 0.7543 (p) cc_final: 0.6957 (t) REVERT: C 927 TYR cc_start: 0.7119 (m-80) cc_final: 0.6895 (m-80) REVERT: C 942 VAL cc_start: 0.8363 (p) cc_final: 0.8095 (t) REVERT: C 948 ILE cc_start: 0.7014 (mm) cc_final: 0.6684 (mm) REVERT: C 989 GLN cc_start: 0.7462 (tt0) cc_final: 0.6780 (tt0) REVERT: C 999 MET cc_start: 0.7223 (mmm) cc_final: 0.6181 (mmm) REVERT: C 1009 ILE cc_start: 0.7941 (tp) cc_final: 0.7238 (tp) REVERT: C 1013 PHE cc_start: 0.6729 (m-80) cc_final: 0.6248 (m-80) REVERT: C 1035 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6825 (mm-40) REVERT: C 1069 ARG cc_start: 0.6915 (mtp180) cc_final: 0.6709 (ptm160) REVERT: C 1083 ILE cc_start: 0.7868 (mt) cc_final: 0.7480 (mm) REVERT: C 1119 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (t) REVERT: C 1124 SER cc_start: 0.7295 (p) cc_final: 0.7007 (p) REVERT: A 28 ASP cc_start: 0.7452 (t0) cc_final: 0.7205 (t0) REVERT: A 47 LEU cc_start: 0.8305 (tp) cc_final: 0.8043 (pp) REVERT: A 297 GLU cc_start: 0.6024 (tt0) cc_final: 0.5597 (tt0) REVERT: A 318 THR cc_start: 0.7738 (m) cc_final: 0.6997 (p) REVERT: A 359 ASN cc_start: 0.7893 (m-40) cc_final: 0.7594 (m-40) REVERT: A 363 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.3330 (p0) REVERT: A 368 MET cc_start: 0.6639 (mtm) cc_final: 0.6390 (mtm) REVERT: A 423 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7447 (tpp80) REVERT: A 447 PHE cc_start: 0.6258 (m-10) cc_final: 0.5997 (m-10) REVERT: A 644 TYR cc_start: 0.7015 (m-80) cc_final: 0.6781 (m-80) REVERT: A 649 ASN cc_start: 0.7857 (m-40) cc_final: 0.7555 (m-40) REVERT: A 671 MET cc_start: 0.7024 (mmm) cc_final: 0.6705 (mmm) REVERT: A 676 TYR cc_start: 0.6633 (t80) cc_final: 0.6418 (t80) REVERT: A 731 ASN cc_start: 0.5946 (t0) cc_final: 0.5573 (t0) REVERT: A 937 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7499 (mmp-170) REVERT: A 942 VAL cc_start: 0.8345 (p) cc_final: 0.7998 (t) REVERT: A 963 TYR cc_start: 0.6329 (m-80) cc_final: 0.5808 (m-80) REVERT: A 1120 LYS cc_start: 0.7167 (mttt) cc_final: 0.6824 (mmmm) outliers start: 112 outliers final: 89 residues processed: 992 average time/residue: 0.4456 time to fit residues: 706.1781 Evaluate side-chains 1024 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 930 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 LEU 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 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1224 MET Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 95 CYS Chi-restraints excluded: chain X residue 111 MET Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 700 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 274 TYR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 373 optimal weight: 0.4980 chunk 245 optimal weight: 0.0370 chunk 396 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 415 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 ASN C 248 HIS C 573 GLN C 851 ASN ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN C1054 ASN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 403 ASN A 590 ASN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33690 Z= 0.204 Angle : 0.670 12.359 45870 Z= 0.351 Chirality : 0.047 0.658 5196 Planarity : 0.004 0.060 5889 Dihedral : 4.941 35.343 4887 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.50 % Allowed : 23.94 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4170 helix: 1.10 (0.19), residues: 744 sheet: -0.04 (0.16), residues: 999 loop : -1.10 (0.13), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 94 HIS 0.026 0.001 HIS A1134 PHE 0.032 0.002 PHE C 285 TYR 0.050 0.002 TYR A 274 ARG 0.015 0.001 ARG B1055 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 936 time to evaluate : 3.584 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: B 47 LEU cc_start: 0.8202 (tp) cc_final: 0.7747 (pp) REVERT: B 96 LEU cc_start: 0.8050 (tp) cc_final: 0.7753 (tt) REVERT: B 108 LYS cc_start: 0.7820 (tttt) cc_final: 0.7512 (tttt) REVERT: B 184 ARG cc_start: 0.6471 (mtt180) cc_final: 0.6057 (mmt90) REVERT: B 213 TYR cc_start: 0.7794 (m-10) cc_final: 0.7434 (m-10) REVERT: B 318 THR cc_start: 0.7554 (m) cc_final: 0.7194 (t) REVERT: B 363 ASN cc_start: 0.4515 (OUTLIER) cc_final: 0.3070 (p0) REVERT: B 447 PHE cc_start: 0.6489 (m-10) cc_final: 0.6254 (m-10) REVERT: B 488 LYS cc_start: 0.8340 (tppt) cc_final: 0.8007 (tppt) REVERT: B 635 ILE cc_start: 0.7973 (mp) cc_final: 0.7595 (pt) REVERT: B 673 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6742 (ttm110) REVERT: B 714 GLN cc_start: 0.7691 (tp40) cc_final: 0.7398 (tm-30) REVERT: B 810 SER cc_start: 0.8045 (p) cc_final: 0.7431 (m) REVERT: B 866 MET cc_start: 0.6261 (tpp) cc_final: 0.5798 (mpp) REVERT: B 882 ASN cc_start: 0.7857 (t0) cc_final: 0.7576 (t0) REVERT: B 949 LYS cc_start: 0.7578 (tppp) cc_final: 0.7138 (ttmm) REVERT: B 963 TYR cc_start: 0.6651 (m-10) cc_final: 0.6237 (m-10) REVERT: B 995 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7449 (mm) REVERT: B 1049 LEU cc_start: 0.8277 (tp) cc_final: 0.7991 (tt) REVERT: B 1134 HIS cc_start: 0.6303 (t-170) cc_final: 0.6036 (t-170) REVERT: B 1150 HIS cc_start: 0.7124 (m90) cc_final: 0.6727 (m-70) REVERT: B 1157 LYS cc_start: 0.7477 (mmmt) cc_final: 0.7006 (mmmt) REVERT: B 1187 ASN cc_start: 0.7734 (m-40) cc_final: 0.7333 (t0) REVERT: X 66 ARG cc_start: 0.5871 (ptm160) cc_final: 0.5623 (tmt170) REVERT: X 109 TYR cc_start: 0.7241 (t80) cc_final: 0.6864 (t80) REVERT: C 24 ASP cc_start: 0.7288 (t0) cc_final: 0.6977 (t0) REVERT: C 88 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6984 (mtt90) REVERT: C 108 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7660 (tmtt) REVERT: C 219 GLU cc_start: 0.5881 (tt0) cc_final: 0.5470 (tt0) REVERT: C 295 MET cc_start: 0.5821 (tpt) cc_final: 0.5577 (tpt) REVERT: C 299 LYS cc_start: 0.7645 (mttt) cc_final: 0.7337 (mttt) REVERT: C 344 LYS cc_start: 0.8392 (ptpt) cc_final: 0.7964 (ptpp) REVERT: C 437 LEU cc_start: 0.8286 (mt) cc_final: 0.7976 (mt) REVERT: C 635 ILE cc_start: 0.8087 (mp) cc_final: 0.7643 (pt) REVERT: C 670 PHE cc_start: 0.8143 (m-80) cc_final: 0.7863 (m-80) REVERT: C 671 MET cc_start: 0.6848 (mmm) cc_final: 0.6543 (mmm) REVERT: C 711 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.6994 (mtm180) REVERT: C 772 GLU cc_start: 0.6640 (tp30) cc_final: 0.6264 (tp30) REVERT: C 809 THR cc_start: 0.7512 (p) cc_final: 0.6931 (t) REVERT: C 927 TYR cc_start: 0.7147 (m-80) cc_final: 0.6938 (m-80) REVERT: C 942 VAL cc_start: 0.8395 (p) cc_final: 0.8172 (t) REVERT: C 989 GLN cc_start: 0.7502 (tt0) cc_final: 0.6669 (tt0) REVERT: C 999 MET cc_start: 0.7212 (mmm) cc_final: 0.6298 (mmm) REVERT: C 1009 ILE cc_start: 0.7959 (tp) cc_final: 0.7263 (tp) REVERT: C 1013 PHE cc_start: 0.6735 (m-80) cc_final: 0.6253 (m-80) REVERT: C 1049 LEU cc_start: 0.8316 (tp) cc_final: 0.8086 (tt) REVERT: C 1083 ILE cc_start: 0.7908 (mt) cc_final: 0.7445 (mm) REVERT: C 1119 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8055 (t) REVERT: C 1124 SER cc_start: 0.7308 (p) cc_final: 0.6995 (p) REVERT: A 24 ASP cc_start: 0.7263 (t0) cc_final: 0.6942 (t0) REVERT: A 28 ASP cc_start: 0.7486 (t0) cc_final: 0.7223 (t0) REVERT: A 47 LEU cc_start: 0.8339 (tp) cc_final: 0.7966 (pp) REVERT: A 313 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6268 (mm-30) REVERT: A 359 ASN cc_start: 0.7874 (m-40) cc_final: 0.7595 (m-40) REVERT: A 363 ASN cc_start: 0.5217 (OUTLIER) cc_final: 0.3720 (p0) REVERT: A 447 PHE cc_start: 0.6284 (m-10) cc_final: 0.5997 (m-10) REVERT: A 562 TYR cc_start: 0.7241 (m-10) cc_final: 0.7011 (m-10) REVERT: A 644 TYR cc_start: 0.7040 (m-80) cc_final: 0.6725 (m-80) REVERT: A 649 ASN cc_start: 0.7816 (m-40) cc_final: 0.7539 (m-40) REVERT: A 671 MET cc_start: 0.7014 (mmm) cc_final: 0.6676 (mmm) REVERT: A 942 VAL cc_start: 0.8338 (p) cc_final: 0.8010 (t) REVERT: A 1120 LYS cc_start: 0.7098 (mttt) cc_final: 0.6802 (mmmm) REVERT: A 1134 HIS cc_start: 0.5836 (t-170) cc_final: 0.5556 (t-170) outliers start: 91 outliers final: 77 residues processed: 967 average time/residue: 0.4639 time to fit residues: 716.9484 Evaluate side-chains 996 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 915 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1224 MET Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 95 CYS Chi-restraints excluded: chain X residue 111 MET Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 700 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1113 GLU Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 274 TYR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1175 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 202 optimal weight: 0.9990 chunk 262 optimal weight: 0.5980 chunk 352 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 331 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 340 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 860 GLN ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS C 573 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN ** C1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 731 ASN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117852 restraints weight = 56676.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122300 restraints weight = 28035.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125273 restraints weight = 16768.879| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 33690 Z= 0.228 Angle : 0.676 12.572 45870 Z= 0.355 Chirality : 0.048 0.640 5196 Planarity : 0.004 0.057 5889 Dihedral : 4.853 31.308 4887 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.58 % Allowed : 24.13 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4170 helix: 1.10 (0.19), residues: 744 sheet: -0.06 (0.16), residues: 1008 loop : -1.14 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 94 HIS 0.025 0.001 HIS A1134 PHE 0.032 0.002 PHE C 285 TYR 0.051 0.002 TYR A 274 ARG 0.015 0.001 ARG B1055 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10712.95 seconds wall clock time: 192 minutes 11.92 seconds (11531.92 seconds total)