Starting phenix.real_space_refine on Wed Jul 24 05:08:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/07_2024/8uk1_42342.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/07_2024/8uk1_42342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/07_2024/8uk1_42342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/07_2024/8uk1_42342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/07_2024/8uk1_42342.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uk1_42342/07_2024/8uk1_42342.cif" } resolution = 3.0 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= 0.065 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 115 5.16 5 C 15810 2.51 5 N 4073 2.21 5 O 4808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 1118": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24806 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8084 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "B" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7988 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 6 Chain: "C" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8090 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 6 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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.56, per 1000 atoms: 0.55 Number of scatterers: 24806 At special positions: 0 Unit cell: (135, 129.6, 172.8, 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 115 16.00 O 4808 8.00 N 4073 7.00 C 15810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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 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 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 I 1 " - " NAG I 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 9.46 Conformation dependent library (CDL) restraints added in 5.0 seconds 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5804 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 44 sheets defined 25.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 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 758 through 783 removed outlier: 3.693A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.096A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.748A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (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 984 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.615A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.744A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.724A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.736A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.777A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.082A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.612A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.156A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.867A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.224A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.516A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.160A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.642A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.080A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.098A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.576A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.933A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.748A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.843A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.903A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.626A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.303A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.726A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.682A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.389A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.797A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.866A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.078A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.563A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 29 removed outlier: 3.665A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.402A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.394A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.330A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.078A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.963A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.131A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.540A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.020A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.713A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.681A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.797A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 645 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.247A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.577A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.073A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.707A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.103A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.602A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 984 hydrogen bonds defined for protein. 2733 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: 10.35 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7891 1.35 - 1.47: 6441 1.47 - 1.60: 10876 1.60 - 1.72: 0 1.72 - 1.85: 142 Bond restraints: 25350 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 25345 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.26: 470 105.26 - 112.64: 13265 112.64 - 120.03: 9056 120.03 - 127.42: 11503 127.42 - 134.80: 187 Bond angle restraints: 34481 Sorted by residual: angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 120.33 124.82 -4.49 8.00e-01 1.56e+00 3.15e+01 angle pdb=" C LEU A 212 " pdb=" N GLU A 213 " pdb=" CA GLU A 213 " ideal model delta sigma weight residual 120.82 128.83 -8.01 1.50e+00 4.44e-01 2.85e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 122.07 129.51 -7.44 1.43e+00 4.89e-01 2.70e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.87 6.36 1.36e+00 5.41e-01 2.19e+01 angle pdb=" C VAL A1040 " pdb=" N ASP A1041 " pdb=" CA ASP A1041 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 ... (remaining 34476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14207 17.56 - 35.12: 1236 35.12 - 52.68: 214 52.68 - 70.25: 56 70.25 - 87.81: 35 Dihedral angle restraints: 15748 sinusoidal: 6730 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 177.12 -84.12 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -7.61 -78.39 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 51.42 41.58 1 1.00e+01 1.00e-02 2.42e+01 ... (remaining 15745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3405 0.073 - 0.146: 620 0.146 - 0.218: 32 0.218 - 0.291: 6 0.291 - 0.364: 1 Chirality restraints: 4064 Sorted by residual: chirality pdb=" C2 NAG C1310 " pdb=" C1 NAG C1310 " pdb=" C3 NAG C1310 " pdb=" N2 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE A 22 " pdb=" CA ILE A 22 " pdb=" CG1 ILE A 22 " pdb=" CG2 ILE A 22 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU C 390 " pdb=" CB LEU C 390 " pdb=" CD1 LEU C 390 " pdb=" CD2 LEU C 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4061 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " -0.054 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 209 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.025 2.00e-02 2.50e+03 2.31e-02 6.68e+00 pdb=" CG ASN A 343 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 745 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" CG ASP B 745 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 745 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 745 " -0.015 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6915 2.82 - 3.34: 19691 3.34 - 3.86: 39901 3.86 - 4.38: 45258 4.38 - 4.90: 81552 Nonbonded interactions: 193317 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.297 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.305 2.440 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.314 2.440 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.314 2.440 ... (remaining 193312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 132 or resid 165 through 677 or resid 690 throu \ gh 1146 or resid 1301 through 1309)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 132 or resid 165 through 677 or resid 690 throu \ gh 1146 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 67.250 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.120 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25350 Z= 0.278 Angle : 0.749 13.392 34481 Z= 0.397 Chirality : 0.053 0.364 4064 Planarity : 0.006 0.084 4395 Dihedral : 13.801 87.806 9818 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3055 helix: -0.23 (0.17), residues: 690 sheet: 0.53 (0.19), residues: 695 loop : -1.34 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 886 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.002 PHE B1121 TYR 0.025 0.001 TYR C 266 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.9057 (ptm) cc_final: 0.8812 (ptm) REVERT: A 821 LEU cc_start: 0.8236 (mt) cc_final: 0.8014 (mp) REVERT: B 935 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 1101 HIS cc_start: 0.7435 (m90) cc_final: 0.7229 (m90) REVERT: C 420 ASP cc_start: 0.7270 (m-30) cc_final: 0.6806 (m-30) REVERT: C 869 MET cc_start: 0.8521 (mtt) cc_final: 0.8279 (mtt) REVERT: C 995 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7321 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 1.1374 time to fit residues: 328.5169 Evaluate side-chains 185 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A 957 GLN A 960 ASN B 394 ASN B1005 GLN C 448 ASN C 493 GLN C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 25350 Z= 0.492 Angle : 0.701 21.021 34481 Z= 0.357 Chirality : 0.051 0.221 4064 Planarity : 0.005 0.068 4395 Dihedral : 7.185 59.438 4282 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.71 % Allowed : 7.65 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3055 helix: 0.75 (0.19), residues: 691 sheet: 0.37 (0.19), residues: 701 loop : -1.33 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 886 HIS 0.009 0.002 HIS B1064 PHE 0.028 0.002 PHE C 377 TYR 0.026 0.002 TYR C1067 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 203 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: A 697 MET cc_start: 0.9136 (ptm) cc_final: 0.8862 (ptm) REVERT: B 375 PHE cc_start: 0.7718 (t80) cc_final: 0.7416 (m-80) REVERT: B 420 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 556 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (p0) REVERT: C 420 ASP cc_start: 0.7091 (m-30) cc_final: 0.6646 (m-30) outliers start: 46 outliers final: 20 residues processed: 231 average time/residue: 1.1631 time to fit residues: 319.1556 Evaluate side-chains 200 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 875 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 232 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 280 optimal weight: 0.4980 chunk 302 optimal weight: 2.9990 chunk 249 optimal weight: 0.4980 chunk 277 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1005 GLN B 52 GLN B 218 GLN B 394 ASN B1005 GLN C 448 ASN C1101 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25350 Z= 0.149 Angle : 0.506 18.735 34481 Z= 0.258 Chirality : 0.044 0.267 4064 Planarity : 0.004 0.052 4395 Dihedral : 6.529 59.286 4282 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.26 % Allowed : 10.51 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3055 helix: 1.66 (0.20), residues: 691 sheet: 0.53 (0.19), residues: 688 loop : -1.13 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS C 66 PHE 0.019 0.001 PHE A 168 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: A 239 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: A 467 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6215 (t70) REVERT: A 697 MET cc_start: 0.9120 (ptm) cc_final: 0.8828 (ptm) REVERT: B 375 PHE cc_start: 0.7511 (t80) cc_final: 0.7216 (m-80) REVERT: B 493 GLN cc_start: 0.7823 (mt0) cc_final: 0.7541 (mt0) REVERT: B 556 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7432 (p0) REVERT: B 560 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7281 (mt) REVERT: B 878 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8006 (mt) REVERT: B 935 GLN cc_start: 0.7676 (tt0) cc_final: 0.7073 (tm-30) REVERT: C 319 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7327 (ttt180) REVERT: C 420 ASP cc_start: 0.7069 (m-30) cc_final: 0.6602 (m-30) REVERT: C 467 ASP cc_start: 0.7805 (t0) cc_final: 0.7459 (m-30) REVERT: C 531 THR cc_start: 0.8052 (m) cc_final: 0.7686 (p) outliers start: 34 outliers final: 11 residues processed: 230 average time/residue: 1.0860 time to fit residues: 300.6881 Evaluate side-chains 205 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.6980 chunk 210 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 266 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 52 GLN B 394 ASN B1005 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25350 Z= 0.219 Angle : 0.533 18.617 34481 Z= 0.270 Chirality : 0.045 0.249 4064 Planarity : 0.004 0.042 4395 Dihedral : 6.416 59.588 4282 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.86 % Allowed : 12.00 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3055 helix: 1.85 (0.20), residues: 691 sheet: 0.54 (0.19), residues: 691 loop : -1.07 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.007 0.001 HIS A 339 PHE 0.025 0.001 PHE C 168 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 190 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7032 (mtp85) REVERT: A 239 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6581 (mp10) REVERT: A 467 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6231 (t70) REVERT: A 661 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 697 MET cc_start: 0.9108 (ptm) cc_final: 0.8774 (ptm) REVERT: A 808 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: A 821 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8028 (mt) REVERT: B 375 PHE cc_start: 0.7615 (t80) cc_final: 0.7311 (m-80) REVERT: B 493 GLN cc_start: 0.7714 (mt0) cc_final: 0.7425 (mt0) REVERT: B 556 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7411 (p0) REVERT: B 878 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8036 (mt) REVERT: B 935 GLN cc_start: 0.7779 (tt0) cc_final: 0.7161 (tm-30) REVERT: C 319 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7325 (ttt180) REVERT: C 326 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7340 (mp) REVERT: C 420 ASP cc_start: 0.7185 (m-30) cc_final: 0.6677 (m-30) REVERT: C 531 THR cc_start: 0.8060 (m) cc_final: 0.7747 (p) REVERT: C 571 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7229 (t70) outliers start: 50 outliers final: 25 residues processed: 225 average time/residue: 1.0401 time to fit residues: 282.0033 Evaluate side-chains 219 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 152 optimal weight: 0.0370 chunk 267 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 853 GLN B1005 GLN C 644 GLN C 690 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25350 Z= 0.241 Angle : 0.539 17.934 34481 Z= 0.274 Chirality : 0.045 0.250 4064 Planarity : 0.004 0.041 4395 Dihedral : 6.231 59.755 4282 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.19 % Allowed : 12.44 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3055 helix: 1.83 (0.20), residues: 697 sheet: 0.51 (0.19), residues: 700 loop : -1.08 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.019 0.001 PHE C 377 TYR 0.019 0.001 TYR C 28 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 192 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 190 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.6886 (mtt180) REVERT: A 239 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6491 (mp10) REVERT: A 355 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7380 (ttp-170) REVERT: A 661 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: A 697 MET cc_start: 0.9088 (ptm) cc_final: 0.8835 (ptm) REVERT: A 808 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: B 375 PHE cc_start: 0.7625 (t80) cc_final: 0.7303 (m-80) REVERT: B 493 GLN cc_start: 0.7679 (mt0) cc_final: 0.7395 (mt0) REVERT: B 556 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7388 (p0) REVERT: B 697 MET cc_start: 0.8923 (ptm) cc_final: 0.8722 (ptp) REVERT: B 878 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8032 (mt) REVERT: C 319 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7427 (ttt180) REVERT: C 326 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7336 (mp) REVERT: C 420 ASP cc_start: 0.7177 (m-30) cc_final: 0.6676 (m-30) REVERT: C 531 THR cc_start: 0.8067 (m) cc_final: 0.7835 (p) REVERT: C 571 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7165 (t70) REVERT: C 1127 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7384 (m-30) outliers start: 59 outliers final: 32 residues processed: 230 average time/residue: 0.9956 time to fit residues: 275.6047 Evaluate side-chains 221 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN A 564 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 540 ASN B 853 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25350 Z= 0.263 Angle : 0.549 15.593 34481 Z= 0.281 Chirality : 0.046 0.248 4064 Planarity : 0.004 0.041 4395 Dihedral : 6.176 59.927 4282 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.49 % Allowed : 12.82 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3055 helix: 1.71 (0.20), residues: 705 sheet: 0.54 (0.19), residues: 695 loop : -1.08 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.030 0.001 PHE C 168 TYR 0.020 0.001 TYR C 28 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 186 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: A 190 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.6944 (mtt180) REVERT: A 239 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6547 (mp10) REVERT: A 355 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7297 (ttp-170) REVERT: A 467 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.5996 (m-30) REVERT: A 661 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 697 MET cc_start: 0.9076 (ptm) cc_final: 0.8835 (ptm) REVERT: A 804 GLN cc_start: 0.8373 (mm110) cc_final: 0.7637 (mt0) REVERT: A 808 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: A 1084 ASP cc_start: 0.7410 (t0) cc_final: 0.7079 (t0) REVERT: B 375 PHE cc_start: 0.7642 (t80) cc_final: 0.7318 (m-80) REVERT: B 493 GLN cc_start: 0.7475 (mt0) cc_final: 0.7169 (mt0) REVERT: B 697 MET cc_start: 0.8973 (ptm) cc_final: 0.8760 (ptp) REVERT: B 878 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 319 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7401 (ttt180) REVERT: C 420 ASP cc_start: 0.7181 (m-30) cc_final: 0.6712 (m-30) REVERT: C 531 THR cc_start: 0.8115 (m) cc_final: 0.7892 (p) REVERT: C 571 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7208 (t70) REVERT: C 830 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.6192 (m-30) outliers start: 67 outliers final: 40 residues processed: 231 average time/residue: 1.0314 time to fit residues: 287.9086 Evaluate side-chains 224 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 853 GLN B1005 GLN C 935 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25350 Z= 0.237 Angle : 0.535 16.228 34481 Z= 0.273 Chirality : 0.045 0.249 4064 Planarity : 0.004 0.052 4395 Dihedral : 6.103 59.867 4282 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.41 % Allowed : 13.26 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3055 helix: 1.83 (0.20), residues: 695 sheet: 0.55 (0.19), residues: 698 loop : -1.08 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.020 0.001 PHE A 168 TYR 0.019 0.001 TYR C 28 ARG 0.012 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 183 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: A 190 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.6956 (mtt180) REVERT: A 239 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: A 355 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7270 (ttp-170) REVERT: A 467 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: A 661 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: A 697 MET cc_start: 0.9065 (ptm) cc_final: 0.8827 (ptm) REVERT: A 804 GLN cc_start: 0.8346 (mm110) cc_final: 0.7719 (mt0) REVERT: A 808 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: A 1084 ASP cc_start: 0.7506 (t0) cc_final: 0.7211 (t0) REVERT: B 32 PHE cc_start: 0.6453 (m-80) cc_final: 0.6132 (m-10) REVERT: B 375 PHE cc_start: 0.7640 (t80) cc_final: 0.7255 (m-80) REVERT: B 493 GLN cc_start: 0.7509 (mt0) cc_final: 0.7211 (mt0) REVERT: B 878 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8047 (mt) REVERT: C 319 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7360 (ttt180) REVERT: C 420 ASP cc_start: 0.7064 (m-30) cc_final: 0.6608 (m-30) REVERT: C 571 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7161 (t70) REVERT: C 830 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.6202 (m-30) REVERT: C 1127 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7494 (m-30) outliers start: 65 outliers final: 41 residues processed: 232 average time/residue: 1.0738 time to fit residues: 299.9876 Evaluate side-chains 231 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 180 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN A 564 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 853 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25350 Z= 0.258 Angle : 0.546 15.428 34481 Z= 0.278 Chirality : 0.045 0.246 4064 Planarity : 0.004 0.041 4395 Dihedral : 6.109 59.977 4282 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.49 % Allowed : 13.41 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3055 helix: 1.82 (0.20), residues: 695 sheet: 0.57 (0.19), residues: 692 loop : -1.06 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.028 0.001 PHE C 168 TYR 0.019 0.001 TYR C 28 ARG 0.007 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 182 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: A 190 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7184 (mtp85) REVERT: A 239 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: A 355 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7292 (ttp-170) REVERT: A 467 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.5998 (m-30) REVERT: A 661 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 697 MET cc_start: 0.9064 (ptm) cc_final: 0.8827 (ptm) REVERT: A 804 GLN cc_start: 0.8342 (mm110) cc_final: 0.7758 (mt0) REVERT: A 808 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: A 1084 ASP cc_start: 0.7546 (t0) cc_final: 0.7291 (t0) REVERT: B 375 PHE cc_start: 0.7649 (t80) cc_final: 0.7248 (m-80) REVERT: B 493 GLN cc_start: 0.7494 (mt0) cc_final: 0.7188 (mt0) REVERT: B 556 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7368 (p0) REVERT: B 878 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8056 (mt) REVERT: C 319 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7410 (ttt180) REVERT: C 420 ASP cc_start: 0.7057 (m-30) cc_final: 0.6629 (m-30) REVERT: C 571 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7188 (t70) REVERT: C 830 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6221 (m-30) REVERT: C 1127 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7493 (m-30) outliers start: 67 outliers final: 45 residues processed: 231 average time/residue: 1.0138 time to fit residues: 282.9064 Evaluate side-chains 237 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 181 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 853 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25350 Z= 0.254 Angle : 0.545 14.477 34481 Z= 0.278 Chirality : 0.045 0.245 4064 Planarity : 0.004 0.040 4395 Dihedral : 6.095 59.915 4282 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.38 % Allowed : 13.71 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3055 helix: 1.83 (0.20), residues: 695 sheet: 0.54 (0.19), residues: 697 loop : -1.04 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.019 0.001 PHE C 377 TYR 0.020 0.001 TYR C 28 ARG 0.006 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 189 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 190 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7199 (mtp85) REVERT: A 239 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7313 (mm110) REVERT: A 355 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: A 467 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.5967 (m-30) REVERT: A 499 PRO cc_start: 0.8334 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: A 661 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 675 GLN cc_start: 0.6355 (pp30) cc_final: 0.6118 (tp40) REVERT: A 697 MET cc_start: 0.9058 (ptm) cc_final: 0.8824 (ptm) REVERT: A 804 GLN cc_start: 0.8292 (mm110) cc_final: 0.7748 (mt0) REVERT: A 808 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: B 375 PHE cc_start: 0.7689 (t80) cc_final: 0.7140 (m-80) REVERT: B 493 GLN cc_start: 0.7457 (mt0) cc_final: 0.7169 (mt0) REVERT: B 878 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8049 (mt) REVERT: C 319 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7406 (ttt180) REVERT: C 420 ASP cc_start: 0.7061 (m-30) cc_final: 0.6626 (m-30) REVERT: C 571 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7201 (t70) REVERT: C 830 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: C 1127 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7493 (m-30) outliers start: 64 outliers final: 46 residues processed: 237 average time/residue: 1.0391 time to fit residues: 298.8415 Evaluate side-chains 240 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 184 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN A 564 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 853 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25350 Z= 0.289 Angle : 0.570 14.149 34481 Z= 0.290 Chirality : 0.046 0.245 4064 Planarity : 0.004 0.054 4395 Dihedral : 6.154 59.960 4282 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.27 % Allowed : 14.19 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3055 helix: 1.74 (0.20), residues: 701 sheet: 0.48 (0.19), residues: 705 loop : -1.04 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.031 0.002 PHE C 168 TYR 0.021 0.001 TYR C 28 ARG 0.012 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 190 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7209 (mtp85) REVERT: A 239 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7400 (mm110) REVERT: A 355 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7376 (ttp-170) REVERT: A 467 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.5976 (m-30) REVERT: A 499 PRO cc_start: 0.8314 (Cg_endo) cc_final: 0.8089 (Cg_exo) REVERT: A 661 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: A 697 MET cc_start: 0.9059 (ptm) cc_final: 0.8831 (ptm) REVERT: A 804 GLN cc_start: 0.8298 (mm110) cc_final: 0.7753 (mt0) REVERT: A 808 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: B 375 PHE cc_start: 0.7700 (t80) cc_final: 0.7148 (m-80) REVERT: B 493 GLN cc_start: 0.7432 (mt0) cc_final: 0.7152 (mt0) REVERT: B 878 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8032 (mt) REVERT: C 319 ARG cc_start: 0.7666 (mmt180) cc_final: 0.7406 (ttt180) REVERT: C 420 ASP cc_start: 0.7064 (m-30) cc_final: 0.6637 (m-30) REVERT: C 571 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7213 (t70) REVERT: C 830 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6227 (m-30) outliers start: 61 outliers final: 46 residues processed: 229 average time/residue: 1.0613 time to fit residues: 292.2207 Evaluate side-chains 234 residues out of total 2692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 556 ASN B 853 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.174990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124023 restraints weight = 26071.764| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.89 r_work: 0.3051 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25350 Z= 0.236 Angle : 0.541 13.643 34481 Z= 0.276 Chirality : 0.045 0.249 4064 Planarity : 0.004 0.040 4395 Dihedral : 6.068 59.856 4282 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.19 % Allowed : 14.52 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3055 helix: 1.83 (0.20), residues: 702 sheet: 0.51 (0.18), residues: 720 loop : -1.05 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.028 0.001 PHE C 168 TYR 0.020 0.001 TYR C 28 ARG 0.009 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.37 seconds wall clock time: 115 minutes 51.20 seconds (6951.20 seconds total)