Starting phenix.real_space_refine on Wed Jul 24 06:16:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0s_42868/07_2024/8v0s_42868.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0s_42868/07_2024/8v0s_42868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0s_42868/07_2024/8v0s_42868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0s_42868/07_2024/8v0s_42868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0s_42868/07_2024/8v0s_42868.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0s_42868/07_2024/8v0s_42868.cif" } resolution = 3.3 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15929 2.51 5 N 4102 2.21 5 O 4805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 24950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "B" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "C" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 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 Time building chain proxies: 13.11, per 1000 atoms: 0.53 Number of scatterers: 24950 At special positions: 0 Unit cell: (141.48, 132.84, 176.04, 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 114 16.00 O 4805 8.00 N 4102 7.00 C 15929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.02 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.03 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 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 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=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C 709 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 717 " Time building additional restraints: 10.67 Conformation dependent library (CDL) restraints added in 4.7 seconds 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 52 sheets defined 22.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.786A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 372' Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.619A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.544A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.976A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.654A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.942A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 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 986 through 1032 Processing helix chain 'A' and resid 1116 through 1120 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.863A pdb=" N ILE B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.746A pdb=" N GLY B 545 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.534A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.629A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1031 Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.515A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.664A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.950A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.793A pdb=" N ALA C 419 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C 420 " --> pdb=" O ASN C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.731A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.572A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.580A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.871A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.594A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 906 removed outlier: 4.001A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 removed outlier: 3.750A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.797A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.672A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 986 through 1032 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.721A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.843A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.830A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 191 removed outlier: 3.560A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 189 through 191 removed outlier: 4.254A pdb=" N PHE A 201 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.649A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.288A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.582A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.184A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.910A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 728 removed outlier: 6.521A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.537A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 4.676A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.950A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.209A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.209A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.658A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.792A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 104 through 107 removed outlier: 4.007A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.611A pdb=" N TYR B 170 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.735A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.993A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.530A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AD2, first strand: chain 'B' and resid 435 through 437 removed outlier: 3.760A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 611 through 613 Processing sheet with id=AD4, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.184A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.241A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.241A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.791A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.553A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.619A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 104 through 105 removed outlier: 3.514A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AE6, first strand: chain 'C' and resid 194 through 197 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.525A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.524A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.041A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.421A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.603A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.592A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.966A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.966A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.644A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.533A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.43 Time building geometry restraints manager: 11.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7850 1.34 - 1.46: 6123 1.46 - 1.58: 11398 1.58 - 1.71: 2 1.71 - 1.83: 141 Bond restraints: 25514 Sorted by residual: bond pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 1.473 1.411 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CB PRO C 225 " pdb=" CG PRO C 225 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 9.02e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.35e+00 ... (remaining 25509 not shown) Histogram of bond angle deviations from ideal: 94.27 - 103.54: 309 103.54 - 112.80: 13588 112.80 - 122.07: 15568 122.07 - 131.33: 5211 131.33 - 140.60: 32 Bond angle restraints: 34708 Sorted by residual: angle pdb=" CA PRO C 225 " pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 112.00 94.86 17.14 1.40e+00 5.10e-01 1.50e+02 angle pdb=" C GLY A1131 " pdb=" N ILE A1132 " pdb=" CA ILE A1132 " ideal model delta sigma weight residual 121.97 133.66 -11.69 1.80e+00 3.09e-01 4.22e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 111.01 121.08 -10.07 1.86e+00 2.89e-01 2.93e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 123.31 -10.97 2.04e+00 2.40e-01 2.89e+01 angle pdb=" C GLY A1099 " pdb=" N THR A1100 " pdb=" CA THR A1100 " ideal model delta sigma weight residual 121.54 131.65 -10.11 1.91e+00 2.74e-01 2.80e+01 ... (remaining 34703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.54: 14005 18.54 - 37.08: 1402 37.08 - 55.62: 232 55.62 - 74.15: 41 74.15 - 92.69: 25 Dihedral angle restraints: 15705 sinusoidal: 6591 harmonic: 9114 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -0.11 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -159.69 73.69 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -12.51 -73.49 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 15702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3954 0.141 - 0.282: 82 0.282 - 0.422: 6 0.422 - 0.563: 5 0.563 - 0.704: 2 Chirality restraints: 4049 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 4046 not shown) Planarity restraints: 4472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " 0.078 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO C 225 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.007 2.00e-02 2.50e+03 3.59e-02 1.61e+01 pdb=" CG ASN C 61 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.039 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 433 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C VAL C 433 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL C 433 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE C 434 " -0.021 2.00e-02 2.50e+03 ... (remaining 4469 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5776 2.79 - 3.32: 21305 3.32 - 3.85: 40708 3.85 - 4.37: 45329 4.37 - 4.90: 79684 Nonbonded interactions: 192802 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR C 393 " pdb=" O HIS C 519 " model vdw 2.279 2.440 nonbonded pdb=" O LEU A 966 " pdb=" OG SER A 975 " model vdw 2.288 2.440 nonbonded pdb=" OE1 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.295 2.440 nonbonded pdb=" O SER B 758 " pdb=" OG SER B 758 " model vdw 2.297 2.440 ... (remaining 192797 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 1148 or resid 1301 through 1307)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 1148 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 66.050 Find NCS groups from input model: 2.140 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: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 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 : 0.005 0.150 25514 Z= 0.303 Angle : 0.883 19.188 34708 Z= 0.453 Chirality : 0.061 0.704 4049 Planarity : 0.007 0.107 4441 Dihedral : 14.639 92.693 9717 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.37 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -3.00 (0.13), residues: 3084 helix: -1.34 (0.16), residues: 631 sheet: -1.60 (0.28), residues: 348 loop : -2.43 (0.12), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.028 0.001 HIS A 954 PHE 0.037 0.002 PHE C 592 TYR 0.027 0.002 TYR C 170 ARG 0.016 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.772 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7567 (m-90) cc_final: 0.6883 (m-90) REVERT: A 904 TYR cc_start: 0.7406 (m-10) cc_final: 0.6971 (m-10) REVERT: B 556 ASN cc_start: 0.7749 (p0) cc_final: 0.7418 (p0) REVERT: B 1138 TYR cc_start: 0.6128 (t80) cc_final: 0.5811 (t80) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3263 time to fit residues: 158.7357 Evaluate side-chains 203 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 0.3980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS B 913 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 960 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25514 Z= 0.302 Angle : 0.634 18.290 34708 Z= 0.326 Chirality : 0.049 0.497 4049 Planarity : 0.005 0.068 4441 Dihedral : 6.693 54.929 4122 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.85 % Favored : 91.05 % Rotamer: Outliers : 1.58 % Allowed : 9.60 % Favored : 88.82 % 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: -2.64 (0.14), residues: 3084 helix: -0.36 (0.18), residues: 649 sheet: -1.91 (0.25), residues: 420 loop : -2.33 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 64 HIS 0.014 0.001 HIS A 954 PHE 0.023 0.002 PHE A 906 TYR 0.029 0.002 TYR B1067 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 232 time to evaluate : 2.993 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7402 (mt) cc_final: 0.7147 (mt) REVERT: A 104 TRP cc_start: 0.7738 (m-90) cc_final: 0.7189 (m-90) REVERT: A 465 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 493 GLN cc_start: 0.6937 (tm-30) cc_final: 0.6656 (tm-30) REVERT: A 904 TYR cc_start: 0.7294 (m-10) cc_final: 0.6888 (m-10) REVERT: C 559 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6878 (t80) REVERT: C 986 LYS cc_start: 0.7434 (mtpp) cc_final: 0.7162 (tptp) outliers start: 43 outliers final: 35 residues processed: 259 average time/residue: 0.3326 time to fit residues: 142.1720 Evaluate side-chains 233 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 0.0370 chunk 306 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 81 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN C 339 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 690 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25514 Z= 0.182 Angle : 0.550 16.442 34708 Z= 0.280 Chirality : 0.046 0.489 4049 Planarity : 0.004 0.064 4441 Dihedral : 6.097 54.011 4122 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 1.36 % Allowed : 12.69 % Favored : 85.95 % 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: -2.34 (0.14), residues: 3084 helix: 0.24 (0.19), residues: 655 sheet: -1.87 (0.24), residues: 439 loop : -2.24 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.010 0.001 HIS A 954 PHE 0.022 0.001 PHE B 342 TYR 0.025 0.001 TYR B 91 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 2.925 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7387 (mt) cc_final: 0.7034 (mt) REVERT: A 104 TRP cc_start: 0.7717 (m-90) cc_final: 0.7230 (m-90) REVERT: A 394 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7403 (m-40) REVERT: A 465 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: A 904 TYR cc_start: 0.7250 (m-10) cc_final: 0.6878 (m-10) REVERT: B 740 MET cc_start: 0.7622 (tpt) cc_final: 0.7331 (tpt) REVERT: C 559 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6970 (t80) REVERT: C 986 LYS cc_start: 0.7498 (mtpp) cc_final: 0.7201 (tptp) outliers start: 37 outliers final: 27 residues processed: 252 average time/residue: 0.3518 time to fit residues: 150.0147 Evaluate side-chains 230 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 301 optimal weight: 0.0270 chunk 148 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 926 GLN B 66 HIS ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25514 Z= 0.208 Angle : 0.551 15.381 34708 Z= 0.281 Chirality : 0.046 0.486 4049 Planarity : 0.004 0.064 4441 Dihedral : 5.861 53.923 4122 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 2.21 % Allowed : 14.28 % Favored : 83.52 % 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: -2.25 (0.14), residues: 3084 helix: 0.58 (0.20), residues: 640 sheet: -2.03 (0.23), residues: 473 loop : -2.20 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.018 0.001 HIS B 66 PHE 0.032 0.001 PHE A 275 TYR 0.028 0.001 TYR B 91 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 210 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7701 (m-90) cc_final: 0.7241 (m-90) REVERT: A 394 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7415 (m-40) REVERT: A 465 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: A 904 TYR cc_start: 0.7282 (m-10) cc_final: 0.6913 (m-10) REVERT: A 1050 MET cc_start: 0.7476 (ptm) cc_final: 0.7111 (ptm) REVERT: B 990 GLU cc_start: 0.6556 (pp20) cc_final: 0.6319 (pp20) REVERT: B 1106 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6885 (pt0) REVERT: B 1138 TYR cc_start: 0.6222 (t80) cc_final: 0.5814 (t80) REVERT: C 338 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.5294 (t80) REVERT: C 559 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6971 (t80) REVERT: C 1089 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.5946 (p90) outliers start: 60 outliers final: 46 residues processed: 254 average time/residue: 0.3207 time to fit residues: 135.6702 Evaluate side-chains 248 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 0.0470 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 0.0070 chunk 270 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 926 GLN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25514 Z= 0.187 Angle : 0.541 13.814 34708 Z= 0.274 Chirality : 0.046 0.487 4049 Planarity : 0.004 0.064 4441 Dihedral : 5.581 53.973 4122 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 2.61 % Allowed : 15.31 % Favored : 82.08 % 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: -2.14 (0.15), residues: 3084 helix: 0.73 (0.20), residues: 649 sheet: -1.99 (0.24), residues: 457 loop : -2.15 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.007 0.001 HIS A 954 PHE 0.026 0.001 PHE A 275 TYR 0.025 0.001 TYR B 91 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 221 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7700 (m-90) cc_final: 0.7197 (m-90) REVERT: A 307 THR cc_start: 0.7973 (m) cc_final: 0.7728 (p) REVERT: A 465 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: A 904 TYR cc_start: 0.7266 (m-10) cc_final: 0.6874 (m-10) REVERT: B 900 MET cc_start: 0.7501 (mtp) cc_final: 0.7088 (mtm) REVERT: B 1106 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: B 1138 TYR cc_start: 0.6227 (t80) cc_final: 0.5790 (t80) REVERT: C 33 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7617 (t) REVERT: C 54 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6224 (pp) REVERT: C 338 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5356 (t80) REVERT: C 559 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.6983 (t80) REVERT: C 1089 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.5996 (p90) outliers start: 71 outliers final: 49 residues processed: 274 average time/residue: 0.3149 time to fit residues: 143.4297 Evaluate side-chains 262 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 926 GLN A1135 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 913 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25514 Z= 0.249 Angle : 0.577 13.844 34708 Z= 0.293 Chirality : 0.047 0.485 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.628 53.533 4122 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.31 % Favored : 90.66 % Rotamer: Outliers : 3.05 % Allowed : 16.11 % Favored : 80.83 % 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: -2.21 (0.15), residues: 3084 helix: 0.60 (0.20), residues: 652 sheet: -2.01 (0.23), residues: 496 loop : -2.17 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.007 0.001 HIS A 954 PHE 0.027 0.002 PHE A 275 TYR 0.025 0.001 TYR B 91 ARG 0.006 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 216 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7701 (m-90) cc_final: 0.7193 (m-90) REVERT: A 307 THR cc_start: 0.8064 (m) cc_final: 0.7827 (p) REVERT: A 319 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7233 (mtp-110) REVERT: A 465 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: A 552 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7922 (mt) REVERT: A 904 TYR cc_start: 0.7328 (m-10) cc_final: 0.6964 (m-10) REVERT: B 900 MET cc_start: 0.7589 (mtp) cc_final: 0.7181 (mtm) REVERT: B 1106 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6912 (pt0) REVERT: B 1138 TYR cc_start: 0.6296 (t80) cc_final: 0.5965 (t80) REVERT: C 24 ARG cc_start: 0.4676 (tpt170) cc_final: 0.4406 (ttt90) REVERT: C 33 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7610 (t) REVERT: C 54 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6270 (pp) REVERT: C 338 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.5379 (t80) REVERT: C 559 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6915 (t80) REVERT: C 1089 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6063 (p90) outliers start: 83 outliers final: 62 residues processed: 283 average time/residue: 0.3106 time to fit residues: 146.6986 Evaluate side-chains 272 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 202 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 170 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1135 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25514 Z= 0.173 Angle : 0.543 12.886 34708 Z= 0.276 Chirality : 0.046 0.487 4049 Planarity : 0.004 0.060 4441 Dihedral : 5.445 54.212 4122 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.11 % Favored : 91.86 % Rotamer: Outliers : 2.28 % Allowed : 17.26 % Favored : 80.46 % 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: -2.03 (0.15), residues: 3084 helix: 0.89 (0.20), residues: 652 sheet: -1.82 (0.24), residues: 463 loop : -2.14 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.006 0.001 HIS A 954 PHE 0.023 0.001 PHE A 275 TYR 0.021 0.001 TYR B 91 ARG 0.006 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7662 (m-90) cc_final: 0.7102 (m-90) REVERT: A 307 THR cc_start: 0.7996 (m) cc_final: 0.7772 (p) REVERT: A 335 LEU cc_start: 0.6280 (mm) cc_final: 0.5619 (tt) REVERT: A 465 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: A 552 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 904 TYR cc_start: 0.7269 (m-10) cc_final: 0.6868 (m-10) REVERT: B 900 MET cc_start: 0.7524 (mtp) cc_final: 0.7124 (mtm) REVERT: B 1106 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: B 1138 TYR cc_start: 0.6364 (t80) cc_final: 0.6017 (t80) REVERT: C 24 ARG cc_start: 0.4640 (tpt170) cc_final: 0.4365 (ttt90) REVERT: C 33 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7670 (t) REVERT: C 54 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6222 (pp) REVERT: C 117 LEU cc_start: 0.3183 (OUTLIER) cc_final: 0.2580 (pt) REVERT: C 338 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.5526 (t80) REVERT: C 559 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6918 (t80) REVERT: C 1089 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5917 (p90) outliers start: 62 outliers final: 44 residues processed: 264 average time/residue: 0.3253 time to fit residues: 143.5076 Evaluate side-chains 253 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 926 GLN A1135 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25514 Z= 0.202 Angle : 0.554 12.456 34708 Z= 0.283 Chirality : 0.046 0.545 4049 Planarity : 0.004 0.060 4441 Dihedral : 5.435 54.006 4122 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.69 % Favored : 91.28 % Rotamer: Outliers : 2.80 % Allowed : 16.96 % Favored : 80.24 % 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: -2.03 (0.15), residues: 3084 helix: 0.85 (0.20), residues: 656 sheet: -1.82 (0.24), residues: 458 loop : -2.13 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS A 954 PHE 0.021 0.001 PHE C1089 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 199 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7683 (m-90) cc_final: 0.7102 (m-90) REVERT: A 307 THR cc_start: 0.8058 (m) cc_final: 0.7831 (p) REVERT: A 332 ILE cc_start: 0.7594 (mp) cc_final: 0.7138 (pt) REVERT: A 465 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: A 552 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 904 TYR cc_start: 0.7285 (m-10) cc_final: 0.6944 (m-10) REVERT: B 900 MET cc_start: 0.7524 (mtp) cc_final: 0.7126 (mtm) REVERT: B 1138 TYR cc_start: 0.6462 (t80) cc_final: 0.6144 (t80) REVERT: C 33 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7692 (t) REVERT: C 54 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6220 (pp) REVERT: C 117 LEU cc_start: 0.3190 (OUTLIER) cc_final: 0.2580 (pt) REVERT: C 338 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.5560 (t80) REVERT: C 403 ARG cc_start: 0.6809 (ttp-170) cc_final: 0.6432 (ttp80) REVERT: C 559 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6937 (t80) REVERT: C 1089 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.5957 (p90) outliers start: 76 outliers final: 58 residues processed: 263 average time/residue: 0.3095 time to fit residues: 136.7527 Evaluate side-chains 259 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 193 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 0.7980 chunk 262 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 0.0870 chunk 279 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1135 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25514 Z= 0.165 Angle : 0.536 11.835 34708 Z= 0.274 Chirality : 0.046 0.503 4049 Planarity : 0.004 0.060 4441 Dihedral : 5.314 54.092 4122 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.30 % Favored : 91.67 % Rotamer: Outliers : 2.32 % Allowed : 17.55 % Favored : 80.13 % 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: -1.93 (0.15), residues: 3084 helix: 0.98 (0.20), residues: 660 sheet: -1.73 (0.25), residues: 457 loop : -2.10 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.005 0.001 HIS A 954 PHE 0.022 0.001 PHE B 342 TYR 0.021 0.001 TYR B 351 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 203 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7629 (m-90) cc_final: 0.7019 (m-90) REVERT: A 278 LYS cc_start: 0.7666 (tppt) cc_final: 0.7112 (tppt) REVERT: A 306 PHE cc_start: 0.7874 (m-80) cc_final: 0.7566 (m-80) REVERT: A 310 LYS cc_start: 0.7510 (ttpt) cc_final: 0.6877 (mmmt) REVERT: A 332 ILE cc_start: 0.7672 (mp) cc_final: 0.7154 (pt) REVERT: A 465 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 552 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7941 (mt) REVERT: A 904 TYR cc_start: 0.7240 (m-10) cc_final: 0.6855 (m-10) REVERT: B 1138 TYR cc_start: 0.6454 (t80) cc_final: 0.6177 (t80) REVERT: C 33 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7734 (t) REVERT: C 54 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6183 (pp) REVERT: C 338 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.5494 (t80) REVERT: C 559 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6955 (t80) REVERT: C 1089 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.5956 (p90) outliers start: 63 outliers final: 50 residues processed: 256 average time/residue: 0.3179 time to fit residues: 137.7251 Evaluate side-chains 253 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 140 optimal weight: 0.0270 chunk 205 optimal weight: 0.0770 chunk 310 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1135 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25514 Z= 0.150 Angle : 0.523 11.425 34708 Z= 0.267 Chirality : 0.045 0.597 4049 Planarity : 0.004 0.060 4441 Dihedral : 5.181 54.543 4122 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.30 % Favored : 91.67 % Rotamer: Outliers : 2.21 % Allowed : 17.92 % Favored : 79.87 % 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: -1.86 (0.15), residues: 3084 helix: 1.13 (0.20), residues: 661 sheet: -1.75 (0.24), residues: 476 loop : -2.06 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS A 954 PHE 0.023 0.001 PHE B 342 TYR 0.021 0.001 TYR B 351 ARG 0.005 0.000 ARG B 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7547 (m-90) cc_final: 0.6938 (m-90) REVERT: A 278 LYS cc_start: 0.7616 (tppt) cc_final: 0.7107 (tppt) REVERT: A 306 PHE cc_start: 0.7839 (m-80) cc_final: 0.7558 (m-80) REVERT: A 310 LYS cc_start: 0.7525 (ttpt) cc_final: 0.6971 (mmmt) REVERT: A 332 ILE cc_start: 0.7717 (mp) cc_final: 0.7247 (pt) REVERT: A 465 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: A 904 TYR cc_start: 0.7190 (m-10) cc_final: 0.6819 (m-10) REVERT: B 740 MET cc_start: 0.7526 (tpt) cc_final: 0.7195 (tpt) REVERT: B 1138 TYR cc_start: 0.6410 (t80) cc_final: 0.6160 (t80) REVERT: C 54 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6156 (pp) REVERT: C 338 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.5443 (t80) REVERT: C 559 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6982 (t80) REVERT: C 900 MET cc_start: 0.6983 (ptp) cc_final: 0.6782 (mtm) REVERT: C 1050 MET cc_start: 0.8073 (ptm) cc_final: 0.7855 (ptm) REVERT: C 1089 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.5917 (p90) outliers start: 60 outliers final: 50 residues processed: 261 average time/residue: 0.3353 time to fit residues: 146.3980 Evaluate side-chains 256 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 644 GLN A 895 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 481 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.184246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151311 restraints weight = 37074.525| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.80 r_work: 0.3638 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25514 Z= 0.388 Angle : 0.680 13.586 34708 Z= 0.349 Chirality : 0.050 0.572 4049 Planarity : 0.005 0.060 4441 Dihedral : 5.853 53.075 4122 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.25 % Favored : 88.68 % Rotamer: Outliers : 2.61 % Allowed : 17.66 % Favored : 79.73 % 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: -2.36 (0.15), residues: 3084 helix: 0.29 (0.20), residues: 660 sheet: -2.01 (0.24), residues: 467 loop : -2.24 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 436 HIS 0.009 0.001 HIS A 954 PHE 0.031 0.002 PHE C1089 TYR 0.030 0.002 TYR B1067 ARG 0.005 0.001 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4870.62 seconds wall clock time: 88 minutes 23.97 seconds (5303.97 seconds total)