Starting phenix.real_space_refine on Mon Feb 19 22:59:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiy_33212/02_2024/7xiy_33212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiy_33212/02_2024/7xiy_33212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiy_33212/02_2024/7xiy_33212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiy_33212/02_2024/7xiy_33212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiy_33212/02_2024/7xiy_33212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiy_33212/02_2024/7xiy_33212.pdb" } resolution = 3.07 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= 0.000 sd= 0.081 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 111 5.16 5 C 16645 2.51 5 N 4277 2.21 5 O 5056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26089 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 8477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8477 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 8477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8477 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8477 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.68, per 1000 atoms: 0.52 Number of scatterers: 26089 At special positions: 0 Unit cell: (148.72, 143.52, 177.84, 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 111 16.00 O 5056 8.00 N 4277 7.00 C 16645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 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-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 343 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B1134 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 9.27 Conformation dependent library (CDL) restraints added in 4.8 seconds 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 47 sheets defined 21.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.842A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.533A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.973A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.684A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.220A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.310A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.785A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) 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 982 removed outlier: 3.729A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 982' Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.074A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 3.946A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 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 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 850 through 856 removed outlier: 3.834A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.524A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.266A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.904A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 982 removed outlier: 3.916A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.114A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1149 removed outlier: 3.654A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.589A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.657A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.563A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.052A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 850 through 856 removed outlier: 3.583A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.393A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.400A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.789A 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 977 through 982 removed outlier: 4.034A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 977 through 982' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.932A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (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 1149 removed outlier: 3.982A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.774A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 131 removed outlier: 3.509A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.994A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.741A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.358A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 538 through 539 removed outlier: 4.826A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.269A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.857A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.791A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.502A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.515A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.558A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AC3, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.341A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AC6, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.870A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.381A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.232A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 659 through 660 removed outlier: 4.424A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.878A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.395A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.395A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.614A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.109A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 126 through 131 removed outlier: 3.533A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 276 through 279 removed outlier: 3.975A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.811A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.132A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.132A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 659 through 660 removed outlier: 4.204A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.829A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.602A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 833 hydrogen bonds defined for protein. 2313 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: 9.83 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 1 1.14 - 1.31: 4219 1.31 - 1.49: 11413 1.49 - 1.67: 10939 1.67 - 1.85: 138 Bond restraints: 26710 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 0.959 0.544 3.40e-02 8.65e+02 2.56e+02 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" CG PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 1.503 1.263 0.240 3.40e-02 8.65e+02 5.00e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 26705 not shown) Histogram of bond angle deviations from ideal: 78.57 - 89.70: 2 89.70 - 100.83: 29 100.83 - 111.96: 13228 111.96 - 123.08: 21162 123.08 - 134.21: 1959 Bond angle restraints: 36380 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 78.57 24.63 1.50e+00 4.44e-01 2.70e+02 angle pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 112.00 94.90 17.10 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 95.40 16.60 1.40e+00 5.10e-01 1.41e+02 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 95.75 16.25 1.40e+00 5.10e-01 1.35e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 96.27 15.73 1.40e+00 5.10e-01 1.26e+02 ... (remaining 36375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 14530 21.85 - 43.69: 1566 43.69 - 65.54: 264 65.54 - 87.39: 63 87.39 - 109.24: 68 Dihedral angle restraints: 16491 sinusoidal: 7008 harmonic: 9483 Sorted by residual: dihedral pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " pdb=" CA PRO C 621 " ideal model delta harmonic sigma weight residual -180.00 -128.61 -51.39 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta harmonic sigma weight residual -180.00 -130.61 -49.39 0 5.00e+00 4.00e-02 9.76e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 4.84 88.16 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 16488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3701 0.082 - 0.163: 511 0.163 - 0.245: 22 0.245 - 0.327: 7 0.327 - 0.408: 5 Chirality restraints: 4246 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" C PRO B 217 " pdb=" CB PRO B 217 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 4243 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.127 5.00e-02 4.00e+02 1.76e-01 4.96e+01 pdb=" N PRO C 373 " 0.304 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.095 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " 0.120 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 217 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.115 5.00e-02 4.00e+02 1.60e-01 4.09e+01 pdb=" N PRO A 384 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.079 5.00e-02 4.00e+02 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6348 2.79 - 3.32: 22774 3.32 - 3.85: 43336 3.85 - 4.37: 47426 4.37 - 4.90: 83683 Nonbonded interactions: 203567 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.266 2.440 nonbonded pdb=" OG SER B 383 " pdb=" OD1 ASP A 985 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD2 ASP C 994 " model vdw 2.281 2.440 nonbonded pdb=" O ILE C 332 " pdb=" NZ LYS C 528 " model vdw 2.284 2.520 nonbonded pdb=" O LEU C 296 " pdb=" OG1 THR C 299 " model vdw 2.285 2.440 ... (remaining 203562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 29 through 1150 or resid 1301 through 1307)) selection = (chain 'C' and (resid 29 through 1150 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.550 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 66.630 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.006 0.544 26710 Z= 0.408 Angle : 0.857 24.629 36380 Z= 0.456 Chirality : 0.054 0.408 4246 Planarity : 0.008 0.176 4655 Dihedral : 19.041 109.237 10296 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.63 % Favored : 92.03 % Rotamer: Outliers : 0.18 % Allowed : 28.57 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3237 helix: 0.09 (0.19), residues: 648 sheet: -1.03 (0.20), residues: 666 loop : -2.49 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 633 HIS 0.009 0.001 HIS B 146 PHE 0.040 0.002 PHE A 338 TYR 0.030 0.001 TYR B 904 ARG 0.009 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 411 time to evaluate : 2.957 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: B 619 GLU cc_start: 0.5812 (mt-10) cc_final: 0.5577 (mp0) REVERT: B 751 ASN cc_start: 0.8384 (m-40) cc_final: 0.8175 (m-40) REVERT: B 869 MET cc_start: 0.8400 (mtm) cc_final: 0.8157 (mtm) REVERT: B 950 ASP cc_start: 0.7251 (m-30) cc_final: 0.6894 (m-30) REVERT: A 645 THR cc_start: 0.8714 (m) cc_final: 0.8491 (p) REVERT: A 697 MET cc_start: 0.7640 (mtp) cc_final: 0.7436 (mtp) REVERT: C 269 TYR cc_start: 0.6986 (m-10) cc_final: 0.6699 (m-10) REVERT: C 271 GLN cc_start: 0.8328 (tt0) cc_final: 0.8021 (mt0) REVERT: C 306 PHE cc_start: 0.8154 (m-80) cc_final: 0.7920 (m-10) REVERT: C 388 ASN cc_start: 0.6830 (p0) cc_final: 0.6131 (p0) REVERT: C 525 CYS cc_start: 0.4790 (p) cc_final: 0.4195 (p) REVERT: C 747 THR cc_start: 0.8092 (t) cc_final: 0.7628 (m) REVERT: C 751 ASN cc_start: 0.8134 (m-40) cc_final: 0.7856 (m110) REVERT: C 759 PHE cc_start: 0.7202 (t80) cc_final: 0.6500 (t80) REVERT: C 869 MET cc_start: 0.8042 (ptp) cc_final: 0.7750 (ptp) REVERT: C 950 ASP cc_start: 0.7340 (m-30) cc_final: 0.7133 (m-30) outliers start: 5 outliers final: 2 residues processed: 415 average time/residue: 0.3868 time to fit residues: 249.9060 Evaluate side-chains 199 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 785 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 755 GLN B 774 GLN B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 872 GLN A 955 ASN C 49 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 675 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 26710 Z= 0.311 Angle : 0.669 10.262 36380 Z= 0.340 Chirality : 0.050 0.351 4246 Planarity : 0.006 0.143 4655 Dihedral : 11.622 95.736 4482 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.94 % Favored : 91.69 % Rotamer: Outliers : 4.23 % Allowed : 25.47 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3237 helix: 0.76 (0.20), residues: 672 sheet: -0.67 (0.21), residues: 591 loop : -2.52 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 633 HIS 0.006 0.001 HIS A1048 PHE 0.020 0.002 PHE C 157 TYR 0.028 0.002 TYR A 904 ARG 0.008 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 238 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 PHE cc_start: 0.4767 (OUTLIER) cc_final: 0.4378 (t80) REVERT: B 619 GLU cc_start: 0.5725 (mt-10) cc_final: 0.5488 (mp0) REVERT: B 751 ASN cc_start: 0.8372 (m-40) cc_final: 0.8044 (m110) REVERT: B 855 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: B 950 ASP cc_start: 0.7455 (m-30) cc_final: 0.6984 (m-30) REVERT: A 329 PHE cc_start: 0.5320 (m-10) cc_final: 0.5043 (m-10) REVERT: A 402 ILE cc_start: 0.2636 (OUTLIER) cc_final: 0.2421 (mt) REVERT: A 645 THR cc_start: 0.8698 (m) cc_final: 0.8433 (p) REVERT: A 979 ASP cc_start: 0.7439 (m-30) cc_final: 0.6821 (t0) REVERT: A 1050 MET cc_start: 0.9013 (ptp) cc_final: 0.8717 (ptp) REVERT: C 104 TRP cc_start: 0.6635 (m-90) cc_final: 0.6269 (m-90) REVERT: C 271 GLN cc_start: 0.8565 (tt0) cc_final: 0.8140 (mt0) REVERT: C 335 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6849 (pp) REVERT: C 388 ASN cc_start: 0.6642 (p0) cc_final: 0.6200 (p0) REVERT: C 525 CYS cc_start: 0.5529 (p) cc_final: 0.5035 (p) REVERT: C 537 LYS cc_start: 0.6987 (tmtt) cc_final: 0.6777 (tttp) REVERT: C 747 THR cc_start: 0.8012 (t) cc_final: 0.7451 (m) REVERT: C 751 ASN cc_start: 0.8103 (m-40) cc_final: 0.7807 (m-40) REVERT: C 918 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7430 (pm20) outliers start: 120 outliers final: 57 residues processed: 342 average time/residue: 0.3309 time to fit residues: 190.0623 Evaluate side-chains 248 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 186 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 244 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1005 GLN A 49 HIS A 61 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 354 ASN C 422 ASN C 613 GLN C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26710 Z= 0.200 Angle : 0.608 11.149 36380 Z= 0.304 Chirality : 0.047 0.330 4246 Planarity : 0.006 0.141 4655 Dihedral : 9.944 91.880 4479 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.48 % Favored : 92.22 % Rotamer: Outliers : 3.63 % Allowed : 25.50 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3237 helix: 1.33 (0.21), residues: 654 sheet: -0.48 (0.21), residues: 567 loop : -2.42 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 633 HIS 0.004 0.001 HIS A 49 PHE 0.016 0.001 PHE A 592 TYR 0.020 0.001 TYR A 904 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 208 time to evaluate : 3.788 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: B 118 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5440 (mt) REVERT: B 198 ASP cc_start: 0.4357 (OUTLIER) cc_final: 0.4061 (m-30) REVERT: B 517 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7271 (mp) REVERT: B 592 PHE cc_start: 0.6483 (t80) cc_final: 0.6236 (t80) REVERT: B 751 ASN cc_start: 0.8239 (m-40) cc_final: 0.7963 (m110) REVERT: B 994 ASP cc_start: 0.8114 (t70) cc_final: 0.7806 (t0) REVERT: A 480 CYS cc_start: 0.2791 (OUTLIER) cc_final: 0.2359 (p) REVERT: A 645 THR cc_start: 0.8624 (m) cc_final: 0.8334 (p) REVERT: A 979 ASP cc_start: 0.7449 (m-30) cc_final: 0.6844 (t0) REVERT: A 1050 MET cc_start: 0.9028 (ptp) cc_final: 0.8817 (ptp) REVERT: C 271 GLN cc_start: 0.8533 (tt0) cc_final: 0.8086 (mt0) REVERT: C 356 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7631 (tptt) REVERT: C 388 ASN cc_start: 0.6483 (p0) cc_final: 0.6053 (p0) REVERT: C 525 CYS cc_start: 0.5337 (p) cc_final: 0.4923 (p) REVERT: C 533 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6967 (tt) REVERT: C 645 THR cc_start: 0.8579 (m) cc_final: 0.8243 (p) REVERT: C 747 THR cc_start: 0.7978 (t) cc_final: 0.7514 (m) REVERT: C 751 ASN cc_start: 0.8077 (m-40) cc_final: 0.7831 (m110) REVERT: C 918 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: C 950 ASP cc_start: 0.7116 (m-30) cc_final: 0.6902 (m-30) REVERT: C 1141 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7620 (tt) outliers start: 103 outliers final: 51 residues processed: 297 average time/residue: 0.3144 time to fit residues: 158.1487 Evaluate side-chains 242 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 184 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9980 chunk 221 optimal weight: 0.0970 chunk 152 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 280 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS A 52 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26710 Z= 0.187 Angle : 0.598 10.109 36380 Z= 0.296 Chirality : 0.047 0.329 4246 Planarity : 0.005 0.140 4655 Dihedral : 8.804 89.519 4479 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.09 % Favored : 91.60 % Rotamer: Outliers : 3.74 % Allowed : 25.15 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3237 helix: 1.45 (0.21), residues: 657 sheet: -0.44 (0.20), residues: 597 loop : -2.41 (0.12), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.004 0.001 HIS A 519 PHE 0.019 0.001 PHE C 592 TYR 0.018 0.001 TYR A 904 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 192 time to evaluate : 3.094 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: B 198 ASP cc_start: 0.4642 (OUTLIER) cc_final: 0.4162 (m-30) REVERT: B 207 HIS cc_start: 0.7316 (m170) cc_final: 0.6979 (m170) REVERT: B 517 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7317 (mp) REVERT: B 748 GLU cc_start: 0.7863 (pm20) cc_final: 0.7367 (pm20) REVERT: B 751 ASN cc_start: 0.8257 (m-40) cc_final: 0.8012 (m110) REVERT: A 78 ARG cc_start: 0.2444 (OUTLIER) cc_final: 0.1556 (mtm-85) REVERT: A 337 PRO cc_start: 0.5825 (Cg_exo) cc_final: 0.5559 (Cg_endo) REVERT: A 356 LYS cc_start: 0.7810 (mptt) cc_final: 0.7565 (mmtt) REVERT: A 480 CYS cc_start: 0.2502 (OUTLIER) cc_final: 0.2034 (p) REVERT: A 645 THR cc_start: 0.8572 (m) cc_final: 0.8276 (p) REVERT: A 979 ASP cc_start: 0.7423 (m-30) cc_final: 0.6845 (t0) REVERT: A 1050 MET cc_start: 0.9103 (ptp) cc_final: 0.8699 (ptm) REVERT: A 1101 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.6003 (p90) REVERT: C 271 GLN cc_start: 0.8511 (tt0) cc_final: 0.8065 (mt0) REVERT: C 356 LYS cc_start: 0.8503 (mmtt) cc_final: 0.7817 (tptt) REVERT: C 525 CYS cc_start: 0.5539 (p) cc_final: 0.5134 (p) REVERT: C 747 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7530 (m) REVERT: C 751 ASN cc_start: 0.8081 (m-40) cc_final: 0.7832 (m110) REVERT: C 918 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: C 950 ASP cc_start: 0.7138 (m-30) cc_final: 0.6783 (m-30) REVERT: C 1144 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7730 (mm-30) outliers start: 106 outliers final: 65 residues processed: 284 average time/residue: 0.3191 time to fit residues: 155.8004 Evaluate side-chains 249 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 176 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.0980 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 0.0000 chunk 233 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 448 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS A 74 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26710 Z= 0.264 Angle : 0.629 9.839 36380 Z= 0.314 Chirality : 0.048 0.326 4246 Planarity : 0.006 0.139 4655 Dihedral : 7.925 86.001 4479 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.40 % Favored : 91.26 % Rotamer: Outliers : 4.87 % Allowed : 24.23 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3237 helix: 1.44 (0.21), residues: 657 sheet: -0.48 (0.19), residues: 636 loop : -2.44 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.006 0.001 HIS B 505 PHE 0.018 0.002 PHE A 374 TYR 0.022 0.001 TYR A 904 ARG 0.015 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 190 time to evaluate : 2.901 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: B 207 HIS cc_start: 0.7484 (m170) cc_final: 0.7149 (m170) REVERT: B 517 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7462 (mp) REVERT: B 748 GLU cc_start: 0.7981 (pm20) cc_final: 0.7643 (pm20) REVERT: B 751 ASN cc_start: 0.8268 (m-40) cc_final: 0.8034 (m-40) REVERT: A 78 ARG cc_start: 0.2769 (OUTLIER) cc_final: 0.1750 (mtm-85) REVERT: A 191 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 356 LYS cc_start: 0.7811 (mptt) cc_final: 0.7523 (mmtt) REVERT: A 480 CYS cc_start: 0.2416 (OUTLIER) cc_final: 0.1960 (p) REVERT: A 645 THR cc_start: 0.8637 (m) cc_final: 0.8313 (p) REVERT: A 1050 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8797 (ptm) REVERT: C 118 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5800 (mm) REVERT: C 190 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5722 (mmt90) REVERT: C 207 HIS cc_start: 0.8126 (m170) cc_final: 0.7920 (m170) REVERT: C 271 GLN cc_start: 0.8529 (tt0) cc_final: 0.8269 (mt0) REVERT: C 356 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7745 (tptt) REVERT: C 368 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.4877 (mt) REVERT: C 525 CYS cc_start: 0.5707 (p) cc_final: 0.5347 (p) REVERT: C 747 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7470 (m) REVERT: C 751 ASN cc_start: 0.8188 (m-40) cc_final: 0.7888 (m-40) REVERT: C 918 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: C 1144 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7740 (mm-30) outliers start: 138 outliers final: 88 residues processed: 309 average time/residue: 0.3208 time to fit residues: 169.4845 Evaluate side-chains 271 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 173 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 4.9990 chunk 282 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 313 optimal weight: 0.3980 chunk 260 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26710 Z= 0.152 Angle : 0.580 9.494 36380 Z= 0.288 Chirality : 0.046 0.319 4246 Planarity : 0.006 0.140 4655 Dihedral : 7.157 83.322 4479 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.69 % Favored : 92.03 % Rotamer: Outliers : 3.53 % Allowed : 26.28 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3237 helix: 1.67 (0.21), residues: 660 sheet: -0.41 (0.19), residues: 633 loop : -2.37 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.008 0.001 HIS A1101 PHE 0.018 0.001 PHE A 220 TYR 0.015 0.001 TYR A 904 ARG 0.004 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 180 time to evaluate : 2.973 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: B 207 HIS cc_start: 0.7474 (m170) cc_final: 0.7132 (m170) REVERT: B 748 GLU cc_start: 0.7888 (pm20) cc_final: 0.7422 (pm20) REVERT: A 191 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7111 (mm-30) REVERT: A 290 ASP cc_start: 0.7044 (p0) cc_final: 0.6835 (p0) REVERT: A 356 LYS cc_start: 0.7766 (mptt) cc_final: 0.7531 (mmtt) REVERT: A 480 CYS cc_start: 0.2293 (OUTLIER) cc_final: 0.1826 (p) REVERT: A 645 THR cc_start: 0.8610 (m) cc_final: 0.8308 (p) REVERT: C 190 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5633 (mmt90) REVERT: C 207 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7179 (m170) REVERT: C 356 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7696 (tptt) REVERT: C 368 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5263 (mp) REVERT: C 525 CYS cc_start: 0.5740 (p) cc_final: 0.5317 (p) REVERT: C 747 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7518 (m) REVERT: C 751 ASN cc_start: 0.8165 (m-40) cc_final: 0.7914 (m110) REVERT: C 918 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7403 (pm20) outliers start: 100 outliers final: 62 residues processed: 265 average time/residue: 0.3156 time to fit residues: 143.0007 Evaluate side-chains 241 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 173 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 190 optimal weight: 0.2980 chunk 144 optimal weight: 9.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 580 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26710 Z= 0.254 Angle : 0.608 10.236 36380 Z= 0.302 Chirality : 0.047 0.327 4246 Planarity : 0.006 0.141 4655 Dihedral : 6.901 81.983 4479 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.74 % Favored : 91.01 % Rotamer: Outliers : 4.02 % Allowed : 25.54 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3237 helix: 1.59 (0.21), residues: 657 sheet: -0.43 (0.20), residues: 609 loop : -2.35 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 886 HIS 0.016 0.001 HIS C 207 PHE 0.017 0.001 PHE A 898 TYR 0.026 0.001 TYR A 904 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 176 time to evaluate : 2.862 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: B 207 HIS cc_start: 0.7590 (m170) cc_final: 0.7251 (m170) REVERT: B 517 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 78 ARG cc_start: 0.2644 (OUTLIER) cc_final: 0.1663 (mtm-85) REVERT: A 191 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7003 (mm-30) REVERT: A 290 ASP cc_start: 0.7289 (p0) cc_final: 0.7053 (p0) REVERT: A 356 LYS cc_start: 0.7642 (mptt) cc_final: 0.7402 (mmtt) REVERT: A 480 CYS cc_start: 0.2460 (OUTLIER) cc_final: 0.2006 (p) REVERT: A 645 THR cc_start: 0.8576 (m) cc_final: 0.8266 (p) REVERT: A 751 ASN cc_start: 0.8300 (m110) cc_final: 0.8097 (m110) REVERT: A 765 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7158 (mtm-85) REVERT: C 170 TYR cc_start: 0.7115 (t80) cc_final: 0.6455 (m-80) REVERT: C 356 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7687 (tptt) REVERT: C 368 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5013 (mt) REVERT: C 525 CYS cc_start: 0.5824 (p) cc_final: 0.5392 (p) REVERT: C 747 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7486 (m) REVERT: C 751 ASN cc_start: 0.8213 (m-40) cc_final: 0.7919 (m110) REVERT: C 918 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7355 (pm20) outliers start: 114 outliers final: 85 residues processed: 275 average time/residue: 0.3195 time to fit residues: 149.6441 Evaluate side-chains 259 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 167 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26710 Z= 0.179 Angle : 0.587 10.007 36380 Z= 0.293 Chirality : 0.046 0.321 4246 Planarity : 0.006 0.141 4655 Dihedral : 6.513 79.875 4479 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.03 % Favored : 91.72 % Rotamer: Outliers : 3.81 % Allowed : 25.82 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3237 helix: 1.68 (0.21), residues: 657 sheet: -0.19 (0.19), residues: 600 loop : -2.31 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.005 0.001 HIS A 207 PHE 0.014 0.001 PHE B 592 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 174 time to evaluate : 2.978 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: B 207 HIS cc_start: 0.7660 (m170) cc_final: 0.7338 (m170) REVERT: A 78 ARG cc_start: 0.2872 (OUTLIER) cc_final: 0.1884 (mtm-85) REVERT: A 191 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6966 (mm-30) REVERT: A 290 ASP cc_start: 0.7275 (p0) cc_final: 0.7044 (p0) REVERT: A 356 LYS cc_start: 0.7595 (mptt) cc_final: 0.7393 (mmtt) REVERT: A 480 CYS cc_start: 0.2279 (OUTLIER) cc_final: 0.1865 (p) REVERT: A 645 THR cc_start: 0.8549 (m) cc_final: 0.8248 (p) REVERT: C 170 TYR cc_start: 0.7142 (t80) cc_final: 0.6494 (m-80) REVERT: C 356 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7635 (tptt) REVERT: C 368 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5272 (mp) REVERT: C 747 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7450 (m) REVERT: C 751 ASN cc_start: 0.8213 (m-40) cc_final: 0.7942 (m110) REVERT: C 918 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: C 979 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7275 (t70) REVERT: C 1101 HIS cc_start: 0.6524 (p90) cc_final: 0.6305 (p90) outliers start: 108 outliers final: 88 residues processed: 267 average time/residue: 0.3110 time to fit residues: 142.5450 Evaluate side-chains 259 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 165 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 291 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 275 optimal weight: 0.0870 chunk 289 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26710 Z= 0.173 Angle : 0.583 9.537 36380 Z= 0.291 Chirality : 0.046 0.320 4246 Planarity : 0.006 0.141 4655 Dihedral : 6.347 78.298 4479 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.46 % Favored : 91.29 % Rotamer: Outliers : 3.63 % Allowed : 26.07 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3237 helix: 1.74 (0.21), residues: 660 sheet: -0.31 (0.20), residues: 609 loop : -2.29 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.009 0.001 HIS C 207 PHE 0.018 0.001 PHE C 329 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 166 time to evaluate : 2.831 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: B 207 HIS cc_start: 0.7639 (m170) cc_final: 0.7314 (m170) REVERT: A 78 ARG cc_start: 0.2870 (OUTLIER) cc_final: 0.1890 (mtm-85) REVERT: A 191 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6973 (mm-30) REVERT: A 290 ASP cc_start: 0.7304 (p0) cc_final: 0.7051 (p0) REVERT: A 480 CYS cc_start: 0.2297 (OUTLIER) cc_final: 0.1848 (p) REVERT: A 540 ASN cc_start: 0.7307 (m-40) cc_final: 0.7008 (m-40) REVERT: A 637 SER cc_start: 0.3687 (OUTLIER) cc_final: 0.3210 (p) REVERT: A 645 THR cc_start: 0.8543 (m) cc_final: 0.8230 (p) REVERT: A 904 TYR cc_start: 0.7175 (m-80) cc_final: 0.6761 (m-80) REVERT: C 170 TYR cc_start: 0.7097 (t80) cc_final: 0.6595 (m-80) REVERT: C 356 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7632 (tptt) REVERT: C 368 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5214 (mt) REVERT: C 747 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7414 (m) REVERT: C 751 ASN cc_start: 0.8210 (m-40) cc_final: 0.7938 (m110) REVERT: C 918 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7357 (pm20) outliers start: 103 outliers final: 88 residues processed: 258 average time/residue: 0.3060 time to fit residues: 136.5823 Evaluate side-chains 257 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 163 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 198 optimal weight: 0.0170 chunk 157 optimal weight: 1.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26710 Z= 0.184 Angle : 0.584 9.567 36380 Z= 0.291 Chirality : 0.046 0.321 4246 Planarity : 0.006 0.142 4655 Dihedral : 6.225 76.998 4479 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.59 % Favored : 91.16 % Rotamer: Outliers : 3.74 % Allowed : 25.82 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3237 helix: 1.74 (0.21), residues: 660 sheet: -0.23 (0.19), residues: 624 loop : -2.29 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.017 0.001 HIS C 207 PHE 0.019 0.001 PHE B 192 TYR 0.015 0.001 TYR B1067 ARG 0.005 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 169 time to evaluate : 3.208 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: B 207 HIS cc_start: 0.7648 (m170) cc_final: 0.7317 (m170) REVERT: B 513 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6579 (tt) REVERT: A 78 ARG cc_start: 0.2838 (OUTLIER) cc_final: 0.1824 (mtm-85) REVERT: A 191 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7000 (mm-30) REVERT: A 290 ASP cc_start: 0.7325 (p0) cc_final: 0.7063 (p0) REVERT: A 480 CYS cc_start: 0.2317 (OUTLIER) cc_final: 0.1841 (p) REVERT: A 540 ASN cc_start: 0.7316 (m-40) cc_final: 0.7012 (m-40) REVERT: A 549 THR cc_start: 0.8401 (p) cc_final: 0.7765 (m) REVERT: A 637 SER cc_start: 0.4000 (OUTLIER) cc_final: 0.3389 (p) REVERT: A 645 THR cc_start: 0.8538 (m) cc_final: 0.8226 (p) REVERT: A 904 TYR cc_start: 0.7173 (m-80) cc_final: 0.6782 (m-80) REVERT: C 170 TYR cc_start: 0.7095 (t80) cc_final: 0.6625 (m-80) REVERT: C 356 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7626 (tptt) REVERT: C 368 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5286 (mp) REVERT: C 747 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7411 (m) REVERT: C 751 ASN cc_start: 0.8218 (m-40) cc_final: 0.7943 (m110) REVERT: C 918 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7359 (pm20) outliers start: 106 outliers final: 96 residues processed: 263 average time/residue: 0.3109 time to fit residues: 141.9254 Evaluate side-chains 267 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 164 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 564 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 784 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.181603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122984 restraints weight = 39518.415| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.84 r_work: 0.3332 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26710 Z= 0.324 Angle : 0.673 11.277 36380 Z= 0.339 Chirality : 0.049 0.322 4246 Planarity : 0.006 0.144 4655 Dihedral : 6.476 76.349 4479 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 4.16 % Allowed : 25.15 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3237 helix: 1.26 (0.21), residues: 675 sheet: -0.58 (0.19), residues: 666 loop : -2.31 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.012 0.001 HIS C 207 PHE 0.026 0.002 PHE A 898 TYR 0.022 0.002 TYR B 396 ARG 0.004 0.001 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5719.97 seconds wall clock time: 105 minutes 48.04 seconds (6348.04 seconds total)