Starting phenix.real_space_refine on Thu Feb 22 03:27:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0q_26263/02_2024/7u0q_26263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0q_26263/02_2024/7u0q_26263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0q_26263/02_2024/7u0q_26263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0q_26263/02_2024/7u0q_26263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0q_26263/02_2024/7u0q_26263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0q_26263/02_2024/7u0q_26263.pdb" } resolution = 3.86 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= -0.003 sd= 0.061 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 137 5.16 5 C 20765 2.51 5 N 5404 2.21 5 O 6415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 101": "OD1" <-> "OD2" Residue "J ASP 105": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32721 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8483 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 58, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8341 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 8508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8508 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 59, 'TRANS': 1027} Chain breaks: 5 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "I" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.69, per 1000 atoms: 0.51 Number of scatterers: 32721 At special positions: 0 Unit cell: (164.641, 162.503, 250.169, 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 137 16.00 O 6415 8.00 N 5404 7.00 C 20765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.32 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.41 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.47 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 17 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 165 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG H 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 709 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 343 " " NAG V 1 " - " ASN C 331 " Time building additional restraints: 12.55 Conformation dependent library (CDL) restraints added in 5.7 seconds 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7670 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 58 sheets defined 22.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.808A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.351A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.359A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.734A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.514A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.115A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.408A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.709A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.587A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.101A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.565A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1033 removed outlier: 4.148A pdb=" N GLU A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.981A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1129 " --> pdb=" O CYS A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1125 through 1129' Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.057A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.768A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.621A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.501A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.784A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.391A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.575A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.642A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.738A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.051A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.522A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.635A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.988A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.061A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.604A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.348A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.589A pdb=" N ARG C 634 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.213A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.599A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.692A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.423A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.202A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 189 removed outlier: 3.777A pdb=" N HIS F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 214 No H-bonds generated for 'chain 'F' and resid 212 through 214' Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.618A pdb=" N GLY G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 189 Processing helix chain 'I' and resid 212 through 214 No H-bonds generated for 'chain 'I' and resid 212 through 214' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.625A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 191 through 195 removed outlier: 4.164A pdb=" N GLY J 194 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.651A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 67 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.921A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 131 current: chain 'A' and resid 151 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 153 current: chain 'A' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.960A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.846A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.085A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.323A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.714A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.866A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A1086 " --> pdb=" O HIS A1083 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.932A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.363A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.875A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 131 current: chain 'B' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.170A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.674A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.722A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.932A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 719 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 719 current: chain 'B' and resid 1059 through 1076 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.425A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.538A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.777A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 151 through 153 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.262A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 326 removed outlier: 4.310A pdb=" N ASN C 540 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER C 325 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN C 542 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.742A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.892A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1077 removed outlier: 3.553A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.655A pdb=" N GLN F 89 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.262A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.605A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.626A pdb=" N GLY G 10 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.227A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER G 181 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER G 183 " --> pdb=" O PHE G 170 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 155 through 157 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.852A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 34 " --> pdb=" O GLN I 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.589A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.775A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU J 18 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 103 through 107 Processing sheet with id=AG3, first strand: chain 'J' and resid 124 through 128 removed outlier: 4.231A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 139 through 149 current: chain 'J' and resid 180 through 189 Processing sheet with id=AG4, first strand: chain 'J' and resid 155 through 158 removed outlier: 3.570A pdb=" N TYR J 198 " --> pdb=" O VAL J 215 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 2922 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: 14.03 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.22: 6 1.22 - 1.54: 33062 1.54 - 1.86: 401 1.86 - 2.18: 0 2.18 - 2.50: 1 Bond restraints: 33470 Sorted by residual: bond pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 1.492 2.503 -1.011 5.00e-02 4.00e+02 4.09e+02 bond pdb=" CG PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 1.503 0.900 0.603 3.40e-02 8.65e+02 3.15e+02 bond pdb=" CB ASN C 439 " pdb=" CG ASN C 439 " ideal model delta sigma weight residual 1.516 1.406 0.110 2.50e-02 1.60e+03 1.93e+01 bond pdb=" N PRO C 987 " pdb=" CA PRO C 987 " ideal model delta sigma weight residual 1.472 1.420 0.051 1.32e-02 5.74e+03 1.51e+01 bond pdb=" CD1 PHE J 67 " pdb=" CE1 PHE J 67 " ideal model delta sigma weight residual 1.382 1.270 0.112 3.00e-02 1.11e+03 1.40e+01 ... (remaining 33465 not shown) Histogram of bond angle deviations from ideal: 0.04 - 29.46: 1 29.46 - 58.88: 0 58.88 - 88.31: 0 88.31 - 117.73: 25218 117.73 - 147.15: 20329 Bond angle restraints: 45548 Sorted by residual: angle pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 112.00 94.80 17.20 1.40e+00 5.10e-01 1.51e+02 angle pdb=" N PRO C 987 " pdb=" CA PRO C 987 " pdb=" CB PRO C 987 " ideal model delta sigma weight residual 103.33 90.46 12.87 1.10e+00 8.26e-01 1.37e+02 angle pdb=" CA PRO C 987 " pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 104.50 89.13 15.37 1.90e+00 2.77e-01 6.54e+01 angle pdb=" N ILE I 29 " pdb=" CA ILE I 29 " pdb=" C ILE I 29 " ideal model delta sigma weight residual 113.53 107.35 6.18 9.80e-01 1.04e+00 3.98e+01 ... (remaining 45543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 19013 22.40 - 44.80: 1292 44.80 - 67.19: 189 67.19 - 89.59: 54 89.59 - 111.99: 6 Dihedral angle restraints: 20554 sinusoidal: 8617 harmonic: 11937 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 152.32 -59.32 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CA ASP J 101 " pdb=" C ASP J 101 " pdb=" N PHE J 102 " pdb=" CA PHE J 102 " ideal model delta harmonic sigma weight residual 180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA PHE J 102 " pdb=" C PHE J 102 " pdb=" N TYR J 103 " pdb=" CA TYR J 103 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 20551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4975 0.098 - 0.197: 308 0.197 - 0.295: 11 0.295 - 0.394: 1 0.394 - 0.492: 2 Chirality restraints: 5297 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5294 not shown) Planarity restraints: 5861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " -0.115 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" CG ASN A1098 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 103 " 0.050 2.00e-02 2.50e+03 2.78e-02 1.55e+01 pdb=" CG TYR J 103 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR J 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR J 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR J 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 103 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR J 103 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 791 " -0.056 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO C 792 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 792 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 792 " -0.046 5.00e-02 4.00e+02 ... (remaining 5858 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 323 2.56 - 3.15: 26845 3.15 - 3.73: 48839 3.73 - 4.32: 65922 4.32 - 4.90: 110085 Nonbonded interactions: 252014 Sorted by model distance: nonbonded pdb=" CG GLN F 166 " pdb=" OH TYR F 173 " model vdw 1.978 3.440 nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 1.981 2.520 nonbonded pdb=" OD2 ASP C 420 " pdb=" ND2 ASN C 460 " model vdw 1.997 2.520 nonbonded pdb=" OH TYR C 421 " pdb=" O ARG C 457 " model vdw 2.000 2.440 nonbonded pdb=" O LEU B 176 " pdb=" NH2 ARG B 190 " model vdw 2.056 2.520 ... (remaining 252009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 741 or resid 743 through 1149 or resid 1301 through \ 1307)) selection = (chain 'B' and (resid 14 through 542 or resid 544 through 623 or resid 633 throu \ gh 741 or resid 743 through 1149 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 542 or resid 544 through 623 or resid 633 through 11 \ 49 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.080 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 84.180 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.350 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 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 : 0.008 1.011 33470 Z= 0.591 Angle : 0.892 106.064 45548 Z= 0.412 Chirality : 0.049 0.492 5297 Planarity : 0.005 0.082 5823 Dihedral : 15.027 111.991 12875 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 0.08 % Allowed : 18.04 % Favored : 81.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.57 % 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: -0.58 (0.13), residues: 4058 helix: 1.08 (0.20), residues: 713 sheet: 0.17 (0.16), residues: 1087 loop : -1.17 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 152 HIS 0.006 0.001 HIS G 204 PHE 0.035 0.002 PHE J 67 TYR 0.055 0.002 TYR J 103 ARG 0.009 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 469 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8575 (pm20) cc_final: 0.8351 (pm20) REVERT: A 121 ASN cc_start: 0.7957 (m110) cc_final: 0.7337 (t0) REVERT: A 532 ASN cc_start: 0.8669 (t0) cc_final: 0.8398 (t0) REVERT: A 558 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8084 (tptt) REVERT: A 663 ASP cc_start: 0.8070 (t0) cc_final: 0.7715 (m-30) REVERT: A 779 GLN cc_start: 0.7894 (tp40) cc_final: 0.7640 (tp40) REVERT: A 904 TYR cc_start: 0.6767 (t80) cc_final: 0.6447 (t80) REVERT: B 129 LYS cc_start: 0.6344 (mttt) cc_final: 0.6112 (ttmt) REVERT: B 131 CYS cc_start: 0.6247 (m) cc_final: 0.5186 (m) REVERT: B 177 MET cc_start: 0.6809 (mtp) cc_final: 0.5135 (ptm) REVERT: B 198 ASP cc_start: 0.8163 (t0) cc_final: 0.7619 (t0) REVERT: B 235 ILE cc_start: 0.6947 (mm) cc_final: 0.6692 (mm) REVERT: B 614 ASP cc_start: 0.7693 (t0) cc_final: 0.7015 (t0) REVERT: B 779 GLN cc_start: 0.8053 (tt0) cc_final: 0.7769 (mt0) REVERT: B 808 ASP cc_start: 0.8083 (t0) cc_final: 0.7742 (t0) REVERT: B 816 SER cc_start: 0.8073 (p) cc_final: 0.7528 (m) REVERT: B 823 PHE cc_start: 0.7061 (t80) cc_final: 0.6781 (m-80) REVERT: B 886 TRP cc_start: 0.8930 (p90) cc_final: 0.7651 (p90) REVERT: B 933 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7431 (tmmt) REVERT: B 984 LEU cc_start: 0.8368 (mt) cc_final: 0.7294 (mp) REVERT: B 1017 GLU cc_start: 0.7555 (tt0) cc_final: 0.7317 (tm-30) REVERT: C 49 HIS cc_start: 0.7521 (t-90) cc_final: 0.7299 (t70) REVERT: C 128 ILE cc_start: 0.8381 (mt) cc_final: 0.7793 (mp) REVERT: C 177 MET cc_start: 0.2111 (mtp) cc_final: 0.1574 (tmm) REVERT: C 202 LYS cc_start: 0.7485 (mttt) cc_final: 0.7054 (mtpt) REVERT: C 317 ASN cc_start: 0.7555 (m-40) cc_final: 0.6770 (m-40) REVERT: C 351 TYR cc_start: 0.7532 (p90) cc_final: 0.7303 (p90) REVERT: C 377 PHE cc_start: 0.8337 (t80) cc_final: 0.8084 (t80) REVERT: C 578 ASP cc_start: 0.8277 (t0) cc_final: 0.7616 (t70) REVERT: C 586 ASP cc_start: 0.8098 (t0) cc_final: 0.7803 (m-30) REVERT: C 731 MET cc_start: 0.7999 (mtm) cc_final: 0.7687 (mtm) REVERT: C 791 THR cc_start: 0.7793 (m) cc_final: 0.7529 (p) REVERT: G 98 ASP cc_start: -0.0710 (OUTLIER) cc_final: -0.1497 (m-30) outliers start: 3 outliers final: 1 residues processed: 471 average time/residue: 0.4585 time to fit residues: 340.7113 Evaluate side-chains 280 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 278 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain G residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 20.0000 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 314 GLN A1058 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1106 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 201 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN I 199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 33470 Z= 0.354 Angle : 0.696 15.478 45548 Z= 0.357 Chirality : 0.048 0.302 5297 Planarity : 0.005 0.049 5823 Dihedral : 7.473 72.961 5553 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 4.27 % Allowed : 16.65 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.63 (0.13), residues: 4058 helix: 0.88 (0.19), residues: 723 sheet: 0.16 (0.15), residues: 1152 loop : -1.21 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 36 HIS 0.007 0.001 HIS C1048 PHE 0.029 0.002 PHE C 168 TYR 0.029 0.002 TYR J 103 ARG 0.006 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 278 time to evaluate : 3.901 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: A 52 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7479 (mt0) REVERT: A 121 ASN cc_start: 0.7771 (m110) cc_final: 0.7141 (t0) REVERT: A 357 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6944 (mtp180) REVERT: A 532 ASN cc_start: 0.8711 (t0) cc_final: 0.8399 (t0) REVERT: A 551 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 654 GLU cc_start: 0.7377 (tp30) cc_final: 0.7088 (pt0) REVERT: A 663 ASP cc_start: 0.8401 (t0) cc_final: 0.7922 (m-30) REVERT: A 726 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8571 (mp) REVERT: A 779 GLN cc_start: 0.7691 (tp40) cc_final: 0.7088 (mm-40) REVERT: A 869 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7228 (ttm) REVERT: A 904 TYR cc_start: 0.6975 (t80) cc_final: 0.6419 (t80) REVERT: A 1077 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7342 (p) REVERT: A 1086 LYS cc_start: 0.7579 (mtmt) cc_final: 0.6680 (pttt) REVERT: B 129 LYS cc_start: 0.6278 (mttt) cc_final: 0.6018 (ttmt) REVERT: B 131 CYS cc_start: 0.5658 (m) cc_final: 0.5039 (m) REVERT: B 198 ASP cc_start: 0.8083 (t0) cc_final: 0.7588 (t0) REVERT: B 235 ILE cc_start: 0.6988 (mm) cc_final: 0.6725 (mm) REVERT: B 614 ASP cc_start: 0.7709 (t0) cc_final: 0.6876 (t0) REVERT: B 779 GLN cc_start: 0.7925 (tt0) cc_final: 0.7449 (mt0) REVERT: B 808 ASP cc_start: 0.8087 (t0) cc_final: 0.7656 (t0) REVERT: B 828 LEU cc_start: 0.5986 (tt) cc_final: 0.5396 (pp) REVERT: B 886 TRP cc_start: 0.8338 (p90) cc_final: 0.7822 (p90) REVERT: B 904 TYR cc_start: 0.6838 (t80) cc_final: 0.6479 (t80) REVERT: B 1017 GLU cc_start: 0.7577 (tt0) cc_final: 0.7306 (tm-30) REVERT: C 49 HIS cc_start: 0.7657 (t-90) cc_final: 0.7434 (t-170) REVERT: C 100 ILE cc_start: 0.8134 (mp) cc_final: 0.7810 (mm) REVERT: C 153 MET cc_start: 0.5080 (pmm) cc_final: 0.4638 (pmm) REVERT: C 177 MET cc_start: 0.2856 (mtp) cc_final: 0.2235 (ttp) REVERT: C 201 PHE cc_start: 0.7574 (t80) cc_final: 0.7368 (t80) REVERT: C 403 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6464 (ptp-170) REVERT: C 578 ASP cc_start: 0.8368 (t0) cc_final: 0.7806 (t70) REVERT: C 586 ASP cc_start: 0.8109 (t0) cc_final: 0.7398 (m-30) REVERT: C 726 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8515 (mm) REVERT: C 791 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7447 (p) REVERT: C 896 ILE cc_start: 0.9334 (tt) cc_final: 0.8987 (mt) REVERT: G 82 MET cc_start: 0.3665 (ttt) cc_final: 0.3336 (ttt) REVERT: G 98 ASP cc_start: -0.0228 (OUTLIER) cc_final: -0.1901 (m-30) outliers start: 153 outliers final: 77 residues processed: 409 average time/residue: 0.4156 time to fit residues: 281.9285 Evaluate side-chains 325 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 240 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 308 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 371 optimal weight: 0.3980 chunk 400 optimal weight: 40.0000 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 30.0000 chunk 126 optimal weight: 0.9990 chunk 297 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4960 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33470 Z= 0.181 Angle : 0.597 16.354 45548 Z= 0.302 Chirality : 0.046 0.283 5297 Planarity : 0.004 0.046 5823 Dihedral : 6.727 56.884 5552 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 3.49 % Allowed : 17.85 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.39 (0.13), residues: 4058 helix: 1.30 (0.20), residues: 712 sheet: 0.30 (0.15), residues: 1135 loop : -1.10 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 353 HIS 0.006 0.001 HIS A1048 PHE 0.029 0.001 PHE F 83 TYR 0.023 0.001 TYR J 103 ARG 0.008 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 273 time to evaluate : 3.560 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: A 121 ASN cc_start: 0.7531 (m110) cc_final: 0.7140 (t0) REVERT: A 532 ASN cc_start: 0.8685 (t0) cc_final: 0.8345 (t0) REVERT: A 551 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7878 (p) REVERT: A 654 GLU cc_start: 0.7345 (tp30) cc_final: 0.7089 (pt0) REVERT: A 663 ASP cc_start: 0.8390 (t0) cc_final: 0.8040 (m-30) REVERT: A 779 GLN cc_start: 0.7654 (tp40) cc_final: 0.7270 (mt0) REVERT: A 855 PHE cc_start: 0.6632 (m-80) cc_final: 0.6382 (m-80) REVERT: A 904 TYR cc_start: 0.6768 (t80) cc_final: 0.6439 (t80) REVERT: A 1086 LYS cc_start: 0.7551 (mtmt) cc_final: 0.6598 (pttp) REVERT: B 129 LYS cc_start: 0.6418 (mttt) cc_final: 0.6175 (ttmt) REVERT: B 131 CYS cc_start: 0.5478 (m) cc_final: 0.4748 (m) REVERT: B 198 ASP cc_start: 0.8136 (t0) cc_final: 0.7654 (t0) REVERT: B 235 ILE cc_start: 0.7002 (mm) cc_final: 0.6725 (mm) REVERT: B 541 PHE cc_start: 0.8914 (p90) cc_final: 0.8708 (p90) REVERT: B 614 ASP cc_start: 0.7526 (t0) cc_final: 0.6821 (t0) REVERT: B 779 GLN cc_start: 0.7889 (tt0) cc_final: 0.7436 (mt0) REVERT: B 787 GLN cc_start: 0.8516 (mp10) cc_final: 0.7792 (mt0) REVERT: B 808 ASP cc_start: 0.8178 (t0) cc_final: 0.7885 (t0) REVERT: B 823 PHE cc_start: 0.6970 (m-80) cc_final: 0.6145 (t80) REVERT: B 828 LEU cc_start: 0.5996 (tt) cc_final: 0.5394 (pp) REVERT: B 886 TRP cc_start: 0.8179 (p90) cc_final: 0.7520 (p90) REVERT: B 904 TYR cc_start: 0.6497 (t80) cc_final: 0.6262 (t80) REVERT: C 49 HIS cc_start: 0.7627 (t-90) cc_final: 0.7327 (t70) REVERT: C 96 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4919 (pp20) REVERT: C 153 MET cc_start: 0.5045 (pmm) cc_final: 0.4666 (pmm) REVERT: C 237 ARG cc_start: 0.8440 (mtm180) cc_final: 0.7656 (ttm170) REVERT: C 578 ASP cc_start: 0.8382 (t0) cc_final: 0.7932 (t70) REVERT: C 586 ASP cc_start: 0.7867 (t0) cc_final: 0.7303 (m-30) REVERT: C 740 MET cc_start: 0.7712 (ttp) cc_final: 0.7506 (ttp) REVERT: C 791 THR cc_start: 0.7768 (m) cc_final: 0.7388 (p) REVERT: C 896 ILE cc_start: 0.9268 (tt) cc_final: 0.8940 (mt) REVERT: G 98 ASP cc_start: -0.0033 (OUTLIER) cc_final: -0.0677 (p0) REVERT: J 82 MET cc_start: 0.3299 (mmt) cc_final: 0.3057 (mmp) outliers start: 125 outliers final: 79 residues processed: 378 average time/residue: 0.4162 time to fit residues: 259.9293 Evaluate side-chains 323 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 241 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 0.0970 chunk 194 optimal weight: 0.0870 chunk 353 optimal weight: 20.0000 chunk 106 optimal weight: 0.0770 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 606 ASN B 23 GLN C 207 HIS C 498 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4955 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33470 Z= 0.170 Angle : 0.577 15.392 45548 Z= 0.289 Chirality : 0.045 0.271 5297 Planarity : 0.004 0.049 5823 Dihedral : 6.356 58.788 5552 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 3.74 % Allowed : 18.18 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.27 (0.13), residues: 4058 helix: 1.57 (0.20), residues: 695 sheet: 0.36 (0.15), residues: 1143 loop : -1.07 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 353 HIS 0.004 0.001 HIS A1048 PHE 0.026 0.001 PHE A 168 TYR 0.021 0.001 TYR I 91 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 261 time to evaluate : 4.121 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: A 52 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7500 (mt0) REVERT: A 121 ASN cc_start: 0.7600 (m110) cc_final: 0.7096 (t0) REVERT: A 532 ASN cc_start: 0.8645 (t0) cc_final: 0.8314 (t0) REVERT: A 551 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 654 GLU cc_start: 0.7328 (tp30) cc_final: 0.7100 (pt0) REVERT: A 705 VAL cc_start: 0.7310 (OUTLIER) cc_final: 0.6506 (t) REVERT: A 779 GLN cc_start: 0.7634 (tp40) cc_final: 0.7258 (mt0) REVERT: A 855 PHE cc_start: 0.6755 (m-80) cc_final: 0.6420 (m-80) REVERT: A 869 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7293 (ttm) REVERT: A 1086 LYS cc_start: 0.7552 (mtmt) cc_final: 0.6623 (pttt) REVERT: B 52 GLN cc_start: 0.8065 (tt0) cc_final: 0.7782 (tm-30) REVERT: B 129 LYS cc_start: 0.6507 (mttt) cc_final: 0.6222 (ttmt) REVERT: B 131 CYS cc_start: 0.5478 (m) cc_final: 0.4618 (m) REVERT: B 198 ASP cc_start: 0.8158 (t0) cc_final: 0.7687 (t0) REVERT: B 614 ASP cc_start: 0.7415 (t0) cc_final: 0.6743 (t0) REVERT: B 779 GLN cc_start: 0.7854 (tt0) cc_final: 0.7326 (mt0) REVERT: B 787 GLN cc_start: 0.8501 (mp10) cc_final: 0.7797 (mt0) REVERT: B 808 ASP cc_start: 0.8151 (t0) cc_final: 0.7810 (t0) REVERT: B 823 PHE cc_start: 0.6974 (m-80) cc_final: 0.6032 (t80) REVERT: B 828 LEU cc_start: 0.6070 (tt) cc_final: 0.5461 (pp) REVERT: B 886 TRP cc_start: 0.8272 (p90) cc_final: 0.7558 (p90) REVERT: B 904 TYR cc_start: 0.6456 (t80) cc_final: 0.6089 (t80) REVERT: C 49 HIS cc_start: 0.7629 (t-90) cc_final: 0.7352 (t70) REVERT: C 117 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7893 (tp) REVERT: C 153 MET cc_start: 0.5085 (pmm) cc_final: 0.4688 (pmm) REVERT: C 196 ASN cc_start: 0.7507 (t0) cc_final: 0.7181 (m-40) REVERT: C 237 ARG cc_start: 0.8419 (mtm180) cc_final: 0.7641 (ttm170) REVERT: C 423 TYR cc_start: 0.7101 (t80) cc_final: 0.6840 (t80) REVERT: C 515 PHE cc_start: 0.8338 (m-80) cc_final: 0.7836 (m-80) REVERT: C 578 ASP cc_start: 0.8397 (t0) cc_final: 0.7949 (t70) REVERT: C 586 ASP cc_start: 0.7767 (t0) cc_final: 0.7242 (m-30) REVERT: C 726 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8273 (mm) REVERT: C 791 THR cc_start: 0.7711 (m) cc_final: 0.7288 (p) REVERT: C 808 ASP cc_start: 0.8090 (t0) cc_final: 0.7748 (t0) REVERT: C 896 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8874 (mt) REVERT: C 976 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7393 (m) REVERT: G 98 ASP cc_start: -0.0122 (OUTLIER) cc_final: -0.0562 (p0) REVERT: J 82 MET cc_start: 0.3390 (mmt) cc_final: 0.3034 (mmp) outliers start: 134 outliers final: 92 residues processed: 372 average time/residue: 0.4094 time to fit residues: 253.5672 Evaluate side-chains 338 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 238 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 30.0000 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 336 optimal weight: 40.0000 chunk 272 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 0.7980 chunk 353 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 33470 Z= 0.332 Angle : 0.641 14.928 45548 Z= 0.324 Chirality : 0.047 0.269 5297 Planarity : 0.004 0.047 5823 Dihedral : 6.391 57.850 5552 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 4.80 % Allowed : 18.01 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.51 (0.13), residues: 4058 helix: 1.13 (0.20), residues: 693 sheet: 0.26 (0.15), residues: 1164 loop : -1.19 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 353 HIS 0.007 0.001 HIS B1064 PHE 0.023 0.002 PHE B 238 TYR 0.032 0.002 TYR C 904 ARG 0.011 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 257 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7893 (p) REVERT: A 58 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: A 121 ASN cc_start: 0.7676 (m110) cc_final: 0.7108 (t0) REVERT: A 235 ILE cc_start: 0.6655 (mm) cc_final: 0.6455 (mm) REVERT: A 532 ASN cc_start: 0.8660 (t0) cc_final: 0.8367 (t0) REVERT: A 551 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 578 ASP cc_start: 0.8188 (t0) cc_final: 0.7912 (p0) REVERT: A 586 ASP cc_start: 0.7545 (m-30) cc_final: 0.7322 (m-30) REVERT: A 705 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.6846 (t) REVERT: A 779 GLN cc_start: 0.7760 (tp40) cc_final: 0.7280 (mt0) REVERT: A 869 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7339 (ttm) REVERT: A 904 TYR cc_start: 0.7084 (t80) cc_final: 0.6659 (t80) REVERT: A 1077 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7467 (p) REVERT: A 1086 LYS cc_start: 0.7683 (mtmt) cc_final: 0.6695 (pttp) REVERT: B 129 LYS cc_start: 0.6310 (mttt) cc_final: 0.5911 (ttmt) REVERT: B 131 CYS cc_start: 0.5613 (m) cc_final: 0.5351 (m) REVERT: B 198 ASP cc_start: 0.8239 (t0) cc_final: 0.7778 (t0) REVERT: B 235 ILE cc_start: 0.6997 (mm) cc_final: 0.6739 (mm) REVERT: B 394 ASN cc_start: 0.6454 (m-40) cc_final: 0.6243 (m-40) REVERT: B 699 LEU cc_start: 0.7733 (mt) cc_final: 0.7506 (mt) REVERT: B 779 GLN cc_start: 0.7758 (tt0) cc_final: 0.7266 (mt0) REVERT: B 787 GLN cc_start: 0.8691 (mp10) cc_final: 0.8157 (mt0) REVERT: B 808 ASP cc_start: 0.8207 (t0) cc_final: 0.7917 (t0) REVERT: B 828 LEU cc_start: 0.6298 (tt) cc_final: 0.5622 (pp) REVERT: B 886 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.7930 (p90) REVERT: B 983 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8049 (mpp-170) REVERT: C 41 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.5910 (mmtt) REVERT: C 49 HIS cc_start: 0.7904 (t-90) cc_final: 0.7563 (t70) REVERT: C 153 MET cc_start: 0.5165 (pmm) cc_final: 0.4770 (pmm) REVERT: C 195 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6744 (mtpt) REVERT: C 196 ASN cc_start: 0.7605 (t0) cc_final: 0.7241 (m-40) REVERT: C 423 TYR cc_start: 0.7066 (t80) cc_final: 0.6861 (t80) REVERT: C 515 PHE cc_start: 0.8452 (m-80) cc_final: 0.7943 (m-80) REVERT: C 578 ASP cc_start: 0.8360 (t0) cc_final: 0.7840 (t0) REVERT: C 586 ASP cc_start: 0.7842 (t0) cc_final: 0.7321 (m-30) REVERT: C 726 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8280 (mm) REVERT: C 808 ASP cc_start: 0.8139 (t0) cc_final: 0.7833 (t0) REVERT: C 901 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6478 (pt0) REVERT: C 981 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6503 (pp) REVERT: F 104 LEU cc_start: 0.1930 (OUTLIER) cc_final: 0.1662 (tp) REVERT: G 98 ASP cc_start: 0.0112 (OUTLIER) cc_final: -0.0452 (p0) outliers start: 172 outliers final: 127 residues processed: 403 average time/residue: 0.4041 time to fit residues: 271.4729 Evaluate side-chains 382 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 242 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.8980 chunk 355 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 30.0000 chunk 327 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 239 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5026 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33470 Z= 0.264 Angle : 0.596 15.176 45548 Z= 0.301 Chirality : 0.045 0.260 5297 Planarity : 0.004 0.061 5823 Dihedral : 6.220 57.543 5552 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 4.63 % Allowed : 18.43 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.47 (0.13), residues: 4058 helix: 1.23 (0.20), residues: 699 sheet: 0.28 (0.15), residues: 1155 loop : -1.18 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 353 HIS 0.005 0.001 HIS B1064 PHE 0.024 0.002 PHE A 168 TYR 0.026 0.001 TYR C 904 ARG 0.008 0.000 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 252 time to evaluate : 3.757 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: A 58 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: A 121 ASN cc_start: 0.7709 (m110) cc_final: 0.7054 (t0) REVERT: A 168 PHE cc_start: 0.7706 (t80) cc_final: 0.7380 (t80) REVERT: A 532 ASN cc_start: 0.8618 (t0) cc_final: 0.8319 (t0) REVERT: A 551 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8062 (p) REVERT: A 578 ASP cc_start: 0.8198 (t0) cc_final: 0.7858 (p0) REVERT: A 586 ASP cc_start: 0.7596 (m-30) cc_final: 0.7336 (m-30) REVERT: A 705 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.6959 (t) REVERT: A 779 GLN cc_start: 0.7708 (tp40) cc_final: 0.7264 (mt0) REVERT: A 904 TYR cc_start: 0.7044 (t80) cc_final: 0.6504 (t80) REVERT: A 1077 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7316 (p) REVERT: A 1086 LYS cc_start: 0.7713 (mtmt) cc_final: 0.6740 (pttt) REVERT: B 52 GLN cc_start: 0.8148 (tt0) cc_final: 0.7746 (tm-30) REVERT: B 129 LYS cc_start: 0.6302 (mttt) cc_final: 0.5900 (ttmt) REVERT: B 131 CYS cc_start: 0.5877 (m) cc_final: 0.5395 (m) REVERT: B 198 ASP cc_start: 0.8155 (t0) cc_final: 0.7657 (t0) REVERT: B 235 ILE cc_start: 0.7012 (mm) cc_final: 0.6743 (mm) REVERT: B 787 GLN cc_start: 0.8683 (mp10) cc_final: 0.8024 (mt0) REVERT: B 828 LEU cc_start: 0.6500 (tt) cc_final: 0.5786 (pp) REVERT: B 886 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7979 (p90) REVERT: B 904 TYR cc_start: 0.7012 (t80) cc_final: 0.6811 (t80) REVERT: C 49 HIS cc_start: 0.7879 (t-90) cc_final: 0.6961 (t-170) REVERT: C 153 MET cc_start: 0.5218 (pmm) cc_final: 0.4805 (pmm) REVERT: C 195 LYS cc_start: 0.7131 (mtpt) cc_final: 0.6869 (mtpt) REVERT: C 237 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7871 (ttm170) REVERT: C 293 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7029 (tt) REVERT: C 403 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6937 (ptp-170) REVERT: C 423 TYR cc_start: 0.7035 (t80) cc_final: 0.6749 (t80) REVERT: C 515 PHE cc_start: 0.8435 (m-80) cc_final: 0.7958 (m-80) REVERT: C 578 ASP cc_start: 0.8408 (t0) cc_final: 0.7928 (t0) REVERT: C 586 ASP cc_start: 0.7834 (t0) cc_final: 0.7351 (m-30) REVERT: C 726 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8242 (mm) REVERT: C 791 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7287 (p) REVERT: F 104 LEU cc_start: 0.1977 (OUTLIER) cc_final: 0.1762 (tp) REVERT: G 98 ASP cc_start: 0.0149 (OUTLIER) cc_final: -0.0253 (p0) outliers start: 166 outliers final: 122 residues processed: 394 average time/residue: 0.3991 time to fit residues: 263.1838 Evaluate side-chains 372 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 240 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 220 optimal weight: 0.0060 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 314 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33470 Z= 0.293 Angle : 0.611 14.948 45548 Z= 0.308 Chirality : 0.046 0.254 5297 Planarity : 0.004 0.061 5823 Dihedral : 6.186 58.010 5552 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 4.80 % Allowed : 18.77 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.55 (0.13), residues: 4058 helix: 1.19 (0.20), residues: 696 sheet: 0.19 (0.15), residues: 1151 loop : -1.21 (0.12), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 353 HIS 0.006 0.001 HIS B1064 PHE 0.030 0.002 PHE B 429 TYR 0.029 0.001 TYR C 904 ARG 0.012 0.000 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 253 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7871 (p) REVERT: A 58 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 121 ASN cc_start: 0.7791 (m110) cc_final: 0.7221 (t0) REVERT: A 168 PHE cc_start: 0.7762 (t80) cc_final: 0.7272 (t80) REVERT: A 532 ASN cc_start: 0.8605 (t0) cc_final: 0.8322 (t0) REVERT: A 578 ASP cc_start: 0.8183 (t0) cc_final: 0.7802 (p0) REVERT: A 586 ASP cc_start: 0.7620 (m-30) cc_final: 0.7328 (m-30) REVERT: A 705 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.6973 (t) REVERT: A 904 TYR cc_start: 0.7200 (t80) cc_final: 0.6612 (t80) REVERT: A 1077 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7393 (p) REVERT: A 1086 LYS cc_start: 0.7740 (mtmt) cc_final: 0.6763 (pttt) REVERT: B 52 GLN cc_start: 0.8124 (tt0) cc_final: 0.7651 (pp30) REVERT: B 129 LYS cc_start: 0.6352 (mttt) cc_final: 0.5925 (ttmt) REVERT: B 131 CYS cc_start: 0.5607 (OUTLIER) cc_final: 0.5048 (m) REVERT: B 198 ASP cc_start: 0.8188 (t0) cc_final: 0.7693 (t0) REVERT: B 235 ILE cc_start: 0.7048 (mm) cc_final: 0.6783 (mm) REVERT: B 356 LYS cc_start: 0.7947 (tptp) cc_final: 0.7725 (mttp) REVERT: B 787 GLN cc_start: 0.8699 (mp10) cc_final: 0.8007 (mt0) REVERT: B 828 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.5881 (pp) REVERT: B 886 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.7849 (p90) REVERT: B 904 TYR cc_start: 0.6994 (t80) cc_final: 0.6701 (t80) REVERT: B 1149 LYS cc_start: 0.3674 (OUTLIER) cc_final: 0.3293 (pttm) REVERT: C 41 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.5727 (mmtt) REVERT: C 49 HIS cc_start: 0.7910 (t-90) cc_final: 0.7017 (t-170) REVERT: C 153 MET cc_start: 0.5291 (pmm) cc_final: 0.4867 (pmm) REVERT: C 196 ASN cc_start: 0.7745 (t0) cc_final: 0.7385 (m-40) REVERT: C 202 LYS cc_start: 0.7525 (mttt) cc_final: 0.7131 (mtpt) REVERT: C 237 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7883 (ttm170) REVERT: C 293 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7352 (tt) REVERT: C 515 PHE cc_start: 0.8418 (m-80) cc_final: 0.7976 (m-80) REVERT: C 578 ASP cc_start: 0.8435 (t0) cc_final: 0.7943 (t0) REVERT: C 586 ASP cc_start: 0.7826 (t0) cc_final: 0.7359 (m-30) REVERT: C 726 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 789 TYR cc_start: 0.8205 (m-80) cc_final: 0.7925 (m-80) REVERT: C 791 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7421 (p) REVERT: C 981 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6424 (pp) outliers start: 172 outliers final: 128 residues processed: 400 average time/residue: 0.4341 time to fit residues: 293.9856 Evaluate side-chains 388 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 247 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 309 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 762 GLN C 23 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 33470 Z= 0.277 Angle : 0.603 14.837 45548 Z= 0.304 Chirality : 0.046 0.272 5297 Planarity : 0.004 0.061 5823 Dihedral : 6.158 57.818 5550 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 4.46 % Allowed : 19.27 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.57 (0.13), residues: 4058 helix: 1.19 (0.20), residues: 699 sheet: 0.18 (0.15), residues: 1151 loop : -1.22 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 353 HIS 0.005 0.001 HIS B1064 PHE 0.045 0.002 PHE B 429 TYR 0.027 0.001 TYR C 904 ARG 0.010 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 255 time to evaluate : 3.887 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: A 58 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: A 121 ASN cc_start: 0.7809 (m110) cc_final: 0.7208 (t0) REVERT: A 532 ASN cc_start: 0.8604 (t0) cc_final: 0.8338 (t0) REVERT: A 578 ASP cc_start: 0.8155 (t0) cc_final: 0.7765 (p0) REVERT: A 586 ASP cc_start: 0.7660 (m-30) cc_final: 0.7352 (m-30) REVERT: A 705 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7012 (t) REVERT: A 904 TYR cc_start: 0.7087 (t80) cc_final: 0.6515 (t80) REVERT: A 1077 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7386 (p) REVERT: A 1086 LYS cc_start: 0.7752 (mtmt) cc_final: 0.6728 (pttp) REVERT: B 52 GLN cc_start: 0.8189 (tt0) cc_final: 0.7706 (pp30) REVERT: B 129 LYS cc_start: 0.6520 (mttt) cc_final: 0.6122 (ttmt) REVERT: B 131 CYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5107 (m) REVERT: B 198 ASP cc_start: 0.8201 (t0) cc_final: 0.7720 (t0) REVERT: B 235 ILE cc_start: 0.7040 (mm) cc_final: 0.6803 (mm) REVERT: B 271 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: B 787 GLN cc_start: 0.8692 (mp10) cc_final: 0.8028 (mt0) REVERT: B 828 LEU cc_start: 0.6717 (tt) cc_final: 0.6005 (pp) REVERT: B 886 TRP cc_start: 0.8507 (OUTLIER) cc_final: 0.7780 (p90) REVERT: B 904 TYR cc_start: 0.6724 (t80) cc_final: 0.6485 (t80) REVERT: B 1149 LYS cc_start: 0.3681 (OUTLIER) cc_final: 0.3382 (pttm) REVERT: C 41 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.5762 (mmtt) REVERT: C 49 HIS cc_start: 0.7927 (t-90) cc_final: 0.7034 (t-170) REVERT: C 153 MET cc_start: 0.5384 (pmm) cc_final: 0.5010 (pmm) REVERT: C 202 LYS cc_start: 0.7508 (mttt) cc_final: 0.7142 (mtpt) REVERT: C 237 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7914 (ttm170) REVERT: C 403 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6840 (ptp-170) REVERT: C 423 TYR cc_start: 0.6721 (t80) cc_final: 0.6464 (t80) REVERT: C 515 PHE cc_start: 0.8442 (m-80) cc_final: 0.8026 (m-80) REVERT: C 578 ASP cc_start: 0.8439 (t0) cc_final: 0.7967 (t0) REVERT: C 586 ASP cc_start: 0.7851 (t0) cc_final: 0.7385 (m-30) REVERT: C 614 ASP cc_start: 0.7256 (t0) cc_final: 0.7047 (t0) REVERT: C 726 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8302 (mm) REVERT: C 789 TYR cc_start: 0.8204 (m-80) cc_final: 0.7926 (m-80) REVERT: C 791 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7409 (p) REVERT: C 981 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6353 (pp) outliers start: 160 outliers final: 130 residues processed: 391 average time/residue: 0.4228 time to fit residues: 274.6721 Evaluate side-chains 386 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 245 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 30.0000 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 0.4980 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 61 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5059 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 33470 Z= 0.318 Angle : 0.623 11.419 45548 Z= 0.314 Chirality : 0.046 0.263 5297 Planarity : 0.004 0.058 5823 Dihedral : 6.200 58.286 5550 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 4.29 % Allowed : 19.55 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.61 (0.13), residues: 4058 helix: 1.12 (0.20), residues: 696 sheet: 0.14 (0.16), residues: 1152 loop : -1.23 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 353 HIS 0.007 0.001 HIS B1064 PHE 0.021 0.002 PHE B 429 TYR 0.030 0.002 TYR C 904 ARG 0.011 0.000 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 247 time to evaluate : 4.061 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: A 51 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 58 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: A 117 LEU cc_start: 0.8080 (tt) cc_final: 0.7537 (mp) REVERT: A 121 ASN cc_start: 0.7789 (m110) cc_final: 0.7149 (t0) REVERT: A 235 ILE cc_start: 0.6694 (mm) cc_final: 0.6489 (mm) REVERT: A 532 ASN cc_start: 0.8616 (t0) cc_final: 0.8349 (t0) REVERT: A 578 ASP cc_start: 0.8185 (t0) cc_final: 0.7753 (p0) REVERT: A 586 ASP cc_start: 0.7623 (m-30) cc_final: 0.7351 (m-30) REVERT: A 705 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7207 (t) REVERT: A 904 TYR cc_start: 0.7270 (t80) cc_final: 0.6668 (t80) REVERT: A 1077 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 1086 LYS cc_start: 0.7724 (mtmt) cc_final: 0.6769 (pttp) REVERT: B 52 GLN cc_start: 0.8105 (tt0) cc_final: 0.7653 (pp30) REVERT: B 129 LYS cc_start: 0.6507 (mttt) cc_final: 0.6114 (ttmt) REVERT: B 131 CYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5250 (m) REVERT: B 198 ASP cc_start: 0.8234 (t0) cc_final: 0.7769 (t0) REVERT: B 235 ILE cc_start: 0.7049 (mm) cc_final: 0.6816 (mm) REVERT: B 271 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: B 787 GLN cc_start: 0.8700 (mp10) cc_final: 0.7952 (mt0) REVERT: B 828 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6167 (pp) REVERT: B 886 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7796 (p90) REVERT: B 904 TYR cc_start: 0.6753 (t80) cc_final: 0.6477 (t80) REVERT: B 1047 TYR cc_start: 0.7827 (m-80) cc_final: 0.7446 (m-80) REVERT: B 1051 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 1149 LYS cc_start: 0.3612 (OUTLIER) cc_final: 0.3286 (pttm) REVERT: C 41 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.5819 (mmtt) REVERT: C 47 VAL cc_start: 0.8511 (t) cc_final: 0.8284 (p) REVERT: C 49 HIS cc_start: 0.7930 (t-90) cc_final: 0.7077 (t-170) REVERT: C 153 MET cc_start: 0.5402 (pmm) cc_final: 0.5048 (pmm) REVERT: C 170 TYR cc_start: 0.8271 (t80) cc_final: 0.7783 (t80) REVERT: C 202 LYS cc_start: 0.7527 (mttt) cc_final: 0.7162 (mtpt) REVERT: C 237 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7919 (ttm170) REVERT: C 403 ARG cc_start: 0.7158 (ptp-170) cc_final: 0.6835 (ptp-170) REVERT: C 578 ASP cc_start: 0.8455 (t0) cc_final: 0.7985 (t0) REVERT: C 586 ASP cc_start: 0.7857 (t0) cc_final: 0.7387 (m-30) REVERT: C 614 ASP cc_start: 0.7252 (t0) cc_final: 0.7049 (t0) REVERT: C 791 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7473 (p) REVERT: C 981 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6469 (pp) REVERT: G 2 VAL cc_start: 0.1516 (t) cc_final: 0.1120 (t) outliers start: 154 outliers final: 128 residues processed: 382 average time/residue: 0.4147 time to fit residues: 267.1289 Evaluate side-chains 381 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 240 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.9990 chunk 387 optimal weight: 40.0000 chunk 236 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33470 Z= 0.274 Angle : 0.607 11.479 45548 Z= 0.306 Chirality : 0.045 0.265 5297 Planarity : 0.004 0.057 5823 Dihedral : 6.155 57.804 5550 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 4.21 % Allowed : 19.85 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.58 (0.13), residues: 4058 helix: 1.22 (0.20), residues: 692 sheet: 0.16 (0.16), residues: 1149 loop : -1.24 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 353 HIS 0.006 0.001 HIS B1064 PHE 0.032 0.002 PHE C 855 TYR 0.030 0.001 TYR C 369 ARG 0.015 0.000 ARG G 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 246 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (p) REVERT: A 117 LEU cc_start: 0.8065 (tt) cc_final: 0.7520 (mp) REVERT: A 121 ASN cc_start: 0.7767 (m110) cc_final: 0.7118 (t0) REVERT: A 235 ILE cc_start: 0.6773 (mm) cc_final: 0.6531 (mm) REVERT: A 532 ASN cc_start: 0.8595 (t0) cc_final: 0.8325 (t0) REVERT: A 578 ASP cc_start: 0.8171 (t0) cc_final: 0.7748 (p0) REVERT: A 586 ASP cc_start: 0.7623 (m-30) cc_final: 0.7345 (m-30) REVERT: A 705 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7192 (t) REVERT: A 904 TYR cc_start: 0.7167 (t80) cc_final: 0.6602 (t80) REVERT: A 1077 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7402 (p) REVERT: A 1086 LYS cc_start: 0.7709 (mtmt) cc_final: 0.6775 (pttp) REVERT: B 52 GLN cc_start: 0.8105 (tt0) cc_final: 0.7658 (pp30) REVERT: B 129 LYS cc_start: 0.6567 (mttt) cc_final: 0.6160 (ttmt) REVERT: B 131 CYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5183 (m) REVERT: B 198 ASP cc_start: 0.8238 (t0) cc_final: 0.7767 (t0) REVERT: B 235 ILE cc_start: 0.7045 (mm) cc_final: 0.6809 (mm) REVERT: B 271 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: B 787 GLN cc_start: 0.8679 (mp10) cc_final: 0.7948 (mt0) REVERT: B 828 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6165 (pp) REVERT: B 886 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.7786 (p90) REVERT: B 904 TYR cc_start: 0.6589 (t80) cc_final: 0.6336 (t80) REVERT: B 1047 TYR cc_start: 0.7902 (m-80) cc_final: 0.7374 (m-80) REVERT: B 1051 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 1149 LYS cc_start: 0.3593 (OUTLIER) cc_final: 0.3314 (pttm) REVERT: C 41 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.5793 (mmtt) REVERT: C 47 VAL cc_start: 0.8550 (t) cc_final: 0.8328 (p) REVERT: C 49 HIS cc_start: 0.7974 (t-90) cc_final: 0.7151 (t-170) REVERT: C 153 MET cc_start: 0.5416 (pmm) cc_final: 0.5066 (pmm) REVERT: C 170 TYR cc_start: 0.8292 (t80) cc_final: 0.7800 (t80) REVERT: C 237 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7936 (ttm170) REVERT: C 369 TYR cc_start: 0.8769 (p90) cc_final: 0.8526 (p90) REVERT: C 403 ARG cc_start: 0.7146 (ptp-170) cc_final: 0.6767 (ptp-170) REVERT: C 515 PHE cc_start: 0.8425 (m-80) cc_final: 0.7843 (m-80) REVERT: C 578 ASP cc_start: 0.8445 (t0) cc_final: 0.7971 (t0) REVERT: C 586 ASP cc_start: 0.7831 (t0) cc_final: 0.7375 (m-30) REVERT: C 981 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6420 (pp) REVERT: G 2 VAL cc_start: 0.1252 (t) cc_final: 0.0874 (t) outliers start: 151 outliers final: 128 residues processed: 378 average time/residue: 0.4083 time to fit residues: 259.5882 Evaluate side-chains 381 residues out of total 3586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 242 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 40.0000 chunk 99 optimal weight: 0.6980 chunk 298 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.208247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.192143 restraints weight = 41762.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.189045 restraints weight = 69234.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.186436 restraints weight = 57279.855| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33470 Z= 0.273 Angle : 0.609 10.929 45548 Z= 0.307 Chirality : 0.045 0.268 5297 Planarity : 0.004 0.054 5823 Dihedral : 6.113 57.536 5550 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 4.02 % Allowed : 19.97 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.60 (0.13), residues: 4058 helix: 1.23 (0.20), residues: 692 sheet: 0.14 (0.15), residues: 1149 loop : -1.25 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 353 HIS 0.005 0.001 HIS B1064 PHE 0.019 0.002 PHE C 392 TYR 0.037 0.001 TYR I 140 ARG 0.015 0.001 ARG G 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6366.70 seconds wall clock time: 118 minutes 4.79 seconds (7084.79 seconds total)