Starting phenix.real_space_refine on Tue Feb 20 01:10:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3n_34470/02_2024/8h3n_34470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3n_34470/02_2024/8h3n_34470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3n_34470/02_2024/8h3n_34470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3n_34470/02_2024/8h3n_34470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3n_34470/02_2024/8h3n_34470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3n_34470/02_2024/8h3n_34470.pdb" } resolution = 2.73 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 16876 2.51 5 N 4346 2.21 5 O 5001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 848": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 70": "OD1" <-> "OD2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26338 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7883 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 54, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 751 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7608 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 52, 'TRANS': 932} Chain breaks: 9 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 7572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7572 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 51, 'TRANS': 925} Chain breaks: 10 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "H" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 661 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.42, per 1000 atoms: 0.51 Number of scatterers: 26338 At special positions: 0 Unit cell: (131.6, 118.816, 187.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 5001 8.00 N 4346 7.00 C 16876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1134 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 717 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 717 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 717 " Time building additional restraints: 10.19 Conformation dependent library (CDL) restraints added in 5.0 seconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6264 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 50 sheets defined 24.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 155 through 158 removed outlier: 3.544A pdb=" N ARG A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.392A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.576A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.670A pdb=" N LYS A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.506A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.248A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.503A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' 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 985 through 1033 removed outlier: 3.805A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.549A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.823A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.467A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.599A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.943A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.180A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.314A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.613A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.782A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.664A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.602A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.186A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.620A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.513A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.550A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.653A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.051A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.766A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.513A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.149A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.531A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.092A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.343A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.782A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.264A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.768A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.792A pdb=" N TYR D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.608A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.928A pdb=" N THR E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 49 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN E 37 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 47 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.680A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.516A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.557A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.449A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.642A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.458A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.600A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.479A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.861A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.543A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.430A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.268A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.207A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.382A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.679A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.806A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AF5, first strand: chain 'I' and resid 62 through 65 removed outlier: 4.009A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2829 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: 13.18 Time building geometry restraints manager: 11.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.31: 4218 1.31 - 1.61: 22589 1.61 - 1.92: 143 1.92 - 2.23: 0 2.23 - 2.53: 1 Bond restraints: 26951 Sorted by residual: bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 2.532 -1.040 5.00e-02 4.00e+02 4.33e+02 bond pdb=" CG PRO E 8 " pdb=" CD PRO E 8 " ideal model delta sigma weight residual 1.503 0.998 0.505 3.40e-02 8.65e+02 2.20e+02 bond pdb=" CG PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.503 1.139 0.364 3.40e-02 8.65e+02 1.14e+02 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta sigma weight residual 1.470 1.434 0.036 1.01e-02 9.80e+03 1.30e+01 ... (remaining 26946 not shown) Histogram of bond angle deviations from ideal: 23.87 - 46.47: 1 46.47 - 69.07: 0 69.07 - 91.67: 2 91.67 - 114.27: 16223 114.27 - 136.87: 20458 Bond angle restraints: 36684 Sorted by residual: angle pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " pdb=" CD PRO E 8 " ideal model delta sigma weight residual 106.10 23.87 82.23 3.20e+00 9.77e-02 6.60e+02 angle pdb=" CA PRO E 8 " pdb=" N PRO E 8 " pdb=" CD PRO E 8 " ideal model delta sigma weight residual 112.00 90.02 21.98 1.40e+00 5.10e-01 2.47e+02 angle pdb=" CA PRO B 209 " pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 112.00 95.09 16.91 1.40e+00 5.10e-01 1.46e+02 angle pdb=" N PRO B 209 " pdb=" CD PRO B 209 " pdb=" CG PRO B 209 " ideal model delta sigma weight residual 103.20 85.72 17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb=" CA PRO E 95 " pdb=" N PRO E 95 " pdb=" CD PRO E 95 " ideal model delta sigma weight residual 111.50 96.33 15.17 1.40e+00 5.10e-01 1.17e+02 ... (remaining 36679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 14513 21.07 - 42.13: 1371 42.13 - 63.20: 362 63.20 - 84.26: 60 84.26 - 105.33: 23 Dihedral angle restraints: 16329 sinusoidal: 6596 harmonic: 9733 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual 180.00 111.99 68.01 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA TYR I 94 " pdb=" C TYR I 94 " pdb=" N PRO I 95 " pdb=" CA PRO I 95 " ideal model delta harmonic sigma weight residual -180.00 -112.14 -67.86 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 172.50 -79.50 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 16326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 4230 0.156 - 0.312: 13 0.312 - 0.467: 0 0.467 - 0.623: 2 0.623 - 0.779: 1 Chirality restraints: 4246 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.36e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 4243 not shown) Planarity restraints: 4705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 7 " -0.128 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO E 8 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " -0.096 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO E 95 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 139 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.047 5.00e-02 4.00e+02 ... (remaining 4702 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 133 2.51 - 3.11: 19800 3.11 - 3.70: 40149 3.70 - 4.30: 60949 4.30 - 4.90: 99735 Nonbonded interactions: 220766 Sorted by model distance: nonbonded pdb=" O PRO B 631 " pdb=" OG1 THR B 632 " model vdw 1.912 2.440 nonbonded pdb=" O3 NAG B1308 " pdb=" O7 NAG B1308 " model vdw 1.981 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.017 2.440 nonbonded pdb=" O GLY B 283 " pdb=" OG1 THR B 284 " model vdw 2.017 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.032 2.440 ... (remaining 220761 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 27 through 140 or resid 164 through 173 or resid 187 throu \ gh 241 or (resid 242 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 264 through 368 or resid 377 through 456 or resid 491 through \ 563 or (resid 564 and (name N or name CA or name C or name O or name CB )) or re \ sid 565 through 567 or (resid 568 and (name N or name CA or name C or name O or \ name CB )) or resid 569 through 570 or (resid 571 through 572 and (name N or nam \ e CA or name C or name O or name CB )) or resid 573 through 620 or resid 629 thr \ ough 1138 or resid 1302 through 1309)) selection = (chain 'B' and (resid 27 through 140 or resid 164 through 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB )) or resid 199 through 368 or \ resid 377 through 620 or resid 629 through 828 or resid 848 through 1138 or res \ id 1302 through 1309)) selection = (chain 'C' and (resid 27 through 173 or resid 187 through 241 or (resid 242 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 264 thr \ ough 456 or resid 491 through 1138 or resid 1301 through 1308)) } 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=0.00 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: 6.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 27.650 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 71.960 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.009 1.040 26951 Z= 0.652 Angle : 0.863 82.227 36684 Z= 0.456 Chirality : 0.050 0.779 4246 Planarity : 0.006 0.173 4678 Dihedral : 17.751 105.330 9942 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.16 % Favored : 92.60 % Rotamer: Outliers : 4.45 % Allowed : 23.50 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3269 helix: 0.95 (0.20), residues: 687 sheet: -0.65 (0.18), residues: 750 loop : -1.80 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 103 HIS 0.008 0.001 HIS B 207 PHE 0.020 0.002 PHE C 186 TYR 0.027 0.002 TYR B 265 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 261 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7881 (p) REVERT: E 79 GLN cc_start: 0.5984 (mt0) cc_final: 0.5753 (mt0) REVERT: B 440 LYS cc_start: 0.5493 (tptt) cc_final: 0.4855 (ttpp) REVERT: C 108 THR cc_start: 0.7482 (p) cc_final: 0.7242 (m) REVERT: C 406 GLU cc_start: 0.6911 (mp0) cc_final: 0.6676 (mp0) REVERT: C 1002 GLN cc_start: 0.8038 (tt0) cc_final: 0.7720 (tm-30) REVERT: H 100 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: I 88 CYS cc_start: 0.3816 (OUTLIER) cc_final: 0.1636 (p) outliers start: 126 outliers final: 102 residues processed: 377 average time/residue: 0.9710 time to fit residues: 456.5618 Evaluate side-chains 347 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 242 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 0.5980 chunk 250 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 300 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 414 GLN A 505 HIS A 607 GLN A 675 GLN A1071 GLN A1101 HIS A1135 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 836 GLN B1101 HIS C 66 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 394 ASN C 755 GLN C1071 GLN C1083 HIS H 79 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26951 Z= 0.320 Angle : 0.660 10.966 36684 Z= 0.347 Chirality : 0.050 0.565 4246 Planarity : 0.005 0.159 4678 Dihedral : 9.763 70.712 4334 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.39 % Favored : 93.42 % Rotamer: Outliers : 6.22 % Allowed : 20.14 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % 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: -1.06 (0.14), residues: 3269 helix: 1.32 (0.20), residues: 686 sheet: -0.58 (0.18), residues: 762 loop : -1.61 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.008 0.001 HIS B 505 PHE 0.021 0.002 PHE E 62 TYR 0.025 0.002 TYR B 265 ARG 0.005 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 255 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.3727 (t80) REVERT: A 470 THR cc_start: 0.8150 (p) cc_final: 0.7932 (p) REVERT: A 994 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7773 (t70) REVERT: E 4 MET cc_start: 0.3713 (mmp) cc_final: 0.2738 (mmp) REVERT: B 278 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8837 (ttpp) REVERT: B 280 ASN cc_start: 0.7478 (t0) cc_final: 0.7149 (t0) REVERT: B 321 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6015 (pm20) REVERT: B 398 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: B 440 LYS cc_start: 0.5446 (tptt) cc_final: 0.4747 (ttpp) REVERT: C 314 GLN cc_start: 0.8664 (mt0) cc_final: 0.8337 (mm-40) REVERT: C 516 GLU cc_start: 0.7037 (tt0) cc_final: 0.6702 (tt0) REVERT: C 907 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8216 (t0) REVERT: H 30 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6180 (p0) REVERT: H 100 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.5380 (m-80) outliers start: 176 outliers final: 101 residues processed: 400 average time/residue: 0.9307 time to fit residues: 460.6567 Evaluate side-chains 347 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 238 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 122 ASN A 675 GLN A 935 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 755 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26951 Z= 0.292 Angle : 0.625 9.640 36684 Z= 0.329 Chirality : 0.049 0.572 4246 Planarity : 0.005 0.124 4678 Dihedral : 8.564 68.209 4271 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.12 % Favored : 93.73 % Rotamer: Outliers : 6.47 % Allowed : 19.86 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3269 helix: 1.45 (0.20), residues: 681 sheet: -0.40 (0.18), residues: 746 loop : -1.51 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.006 0.001 HIS B 505 PHE 0.022 0.002 PHE E 62 TYR 0.022 0.002 TYR C 453 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 251 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7098 (t0) REVERT: A 186 PHE cc_start: 0.4711 (OUTLIER) cc_final: 0.4469 (t80) REVERT: A 470 THR cc_start: 0.8159 (p) cc_final: 0.7954 (p) REVERT: A 557 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7887 (mtmt) REVERT: A 994 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7775 (t70) REVERT: E 4 MET cc_start: 0.3660 (mmp) cc_final: 0.3420 (tpp) REVERT: B 278 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8836 (ttpp) REVERT: B 280 ASN cc_start: 0.7452 (t0) cc_final: 0.7137 (t0) REVERT: B 321 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: B 390 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 398 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6968 (m-30) REVERT: B 440 LYS cc_start: 0.5472 (tptt) cc_final: 0.4701 (ttpp) REVERT: B 532 ASN cc_start: 0.6628 (t0) cc_final: 0.6229 (m-40) REVERT: C 234 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6533 (p0) REVERT: C 314 GLN cc_start: 0.8656 (mt0) cc_final: 0.8359 (mm-40) REVERT: C 516 GLU cc_start: 0.7056 (tt0) cc_final: 0.6715 (tt0) REVERT: C 658 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8030 (m-40) REVERT: C 907 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8221 (t0) REVERT: H 30 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6197 (p0) REVERT: H 100 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: I 47 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6350 (tm) REVERT: I 88 CYS cc_start: 0.4147 (OUTLIER) cc_final: 0.1831 (p) outliers start: 183 outliers final: 111 residues processed: 404 average time/residue: 0.8912 time to fit residues: 450.1707 Evaluate side-chains 358 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 232 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 302 optimal weight: 0.6980 chunk 319 optimal weight: 0.0030 chunk 157 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 935 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 544 ASN B 804 GLN B 836 GLN B 935 GLN B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 755 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26951 Z= 0.170 Angle : 0.549 9.002 36684 Z= 0.289 Chirality : 0.046 0.528 4246 Planarity : 0.005 0.094 4678 Dihedral : 7.707 66.920 4262 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.20 % Favored : 94.65 % Rotamer: Outliers : 5.27 % Allowed : 21.27 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3269 helix: 1.81 (0.20), residues: 672 sheet: -0.31 (0.18), residues: 746 loop : -1.35 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.005 0.001 HIS A1083 PHE 0.014 0.001 PHE H 100H TYR 0.023 0.001 TYR I 94 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 242 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7041 (t0) REVERT: A 470 THR cc_start: 0.8116 (p) cc_final: 0.7915 (p) REVERT: A 755 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7209 (mt0) REVERT: A 759 PHE cc_start: 0.7091 (m-80) cc_final: 0.6811 (m-80) REVERT: A 994 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7806 (t70) REVERT: B 81 ASN cc_start: 0.6900 (p0) cc_final: 0.6489 (p0) REVERT: B 278 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8787 (ttpp) REVERT: B 280 ASN cc_start: 0.7362 (t0) cc_final: 0.7104 (t0) REVERT: B 321 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: B 353 TRP cc_start: 0.6712 (p-90) cc_final: 0.6131 (p-90) REVERT: B 390 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7889 (mt) REVERT: B 398 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: B 429 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5418 (p90) REVERT: B 440 LYS cc_start: 0.5407 (tptt) cc_final: 0.4710 (ttpp) REVERT: B 532 ASN cc_start: 0.6617 (t0) cc_final: 0.6261 (m-40) REVERT: B 675 GLN cc_start: 0.7092 (tp40) cc_final: 0.6825 (tp-100) REVERT: B 745 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6439 (p0) REVERT: B 811 LYS cc_start: 0.7053 (ptpt) cc_final: 0.6831 (mmtp) REVERT: C 314 GLN cc_start: 0.8600 (mt0) cc_final: 0.8320 (mm-40) REVERT: C 516 GLU cc_start: 0.6989 (tt0) cc_final: 0.6728 (tt0) REVERT: C 1002 GLN cc_start: 0.8037 (tt0) cc_final: 0.7730 (tm-30) REVERT: C 1092 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6502 (pp20) REVERT: H 4 LEU cc_start: 0.3474 (OUTLIER) cc_final: 0.3046 (pp) REVERT: H 30 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6479 (p0) REVERT: H 59 TYR cc_start: 0.5024 (m-10) cc_final: 0.4781 (m-10) REVERT: H 100 TYR cc_start: 0.5755 (OUTLIER) cc_final: 0.5209 (m-80) outliers start: 149 outliers final: 87 residues processed: 364 average time/residue: 0.9506 time to fit residues: 426.0574 Evaluate side-chains 327 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 227 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 238 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 675 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 836 GLN B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 321 GLN C 755 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26951 Z= 0.365 Angle : 0.648 10.020 36684 Z= 0.343 Chirality : 0.050 0.567 4246 Planarity : 0.005 0.093 4678 Dihedral : 8.075 68.174 4249 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.61 % Favored : 93.24 % Rotamer: Outliers : 6.43 % Allowed : 20.57 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3269 helix: 1.50 (0.20), residues: 676 sheet: -0.31 (0.18), residues: 772 loop : -1.44 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.005 0.001 HIS C1064 PHE 0.027 0.002 PHE E 62 TYR 0.024 0.002 TYR C 453 ARG 0.004 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 232 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7091 (t0) REVERT: A 186 PHE cc_start: 0.4554 (OUTLIER) cc_final: 0.3940 (t80) REVERT: A 557 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: A 564 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 755 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7250 (mt0) REVERT: A 994 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7788 (t70) REVERT: D 56 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6214 (m-30) REVERT: B 81 ASN cc_start: 0.6986 (p0) cc_final: 0.6511 (p0) REVERT: B 278 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8841 (ttpp) REVERT: B 321 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: B 390 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7883 (mt) REVERT: B 398 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: B 532 ASN cc_start: 0.6566 (t0) cc_final: 0.6317 (m-40) REVERT: B 675 GLN cc_start: 0.7224 (tp40) cc_final: 0.6958 (tp-100) REVERT: B 990 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: C 233 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7997 (pt) REVERT: C 234 ASN cc_start: 0.6927 (OUTLIER) cc_final: 0.6478 (p0) REVERT: C 314 GLN cc_start: 0.8654 (mt0) cc_final: 0.8359 (mm-40) REVERT: C 907 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8228 (t0) REVERT: H 30 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6578 (p0) REVERT: H 100 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: I 47 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6126 (tm) outliers start: 182 outliers final: 118 residues processed: 383 average time/residue: 0.9553 time to fit residues: 458.3164 Evaluate side-chains 359 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 223 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 9.9990 chunk 288 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 320 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 675 GLN A 935 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 836 GLN B 853 GLN B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 755 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26951 Z= 0.207 Angle : 0.572 9.327 36684 Z= 0.301 Chirality : 0.047 0.552 4246 Planarity : 0.005 0.085 4678 Dihedral : 7.609 67.090 4247 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.38 % Favored : 94.43 % Rotamer: Outliers : 5.58 % Allowed : 21.20 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3269 helix: 1.73 (0.20), residues: 671 sheet: -0.20 (0.18), residues: 758 loop : -1.33 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS A 625 PHE 0.015 0.001 PHE E 62 TYR 0.024 0.001 TYR C 453 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 234 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7050 (t0) REVERT: A 557 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7862 (mtmt) REVERT: A 564 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: A 755 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: A 994 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7831 (t70) REVERT: A 1073 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: B 81 ASN cc_start: 0.7008 (p0) cc_final: 0.6542 (p0) REVERT: B 278 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8791 (ttpp) REVERT: B 321 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6109 (pm20) REVERT: B 390 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B 398 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7050 (m-30) REVERT: B 429 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5534 (p90) REVERT: B 532 ASN cc_start: 0.6546 (t0) cc_final: 0.6307 (m-40) REVERT: B 811 LYS cc_start: 0.7135 (ptpt) cc_final: 0.6815 (mmtp) REVERT: C 234 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6522 (p0) REVERT: C 314 GLN cc_start: 0.8613 (mt0) cc_final: 0.8326 (mm-40) REVERT: C 324 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: C 516 GLU cc_start: 0.7051 (tt0) cc_final: 0.6809 (tt0) REVERT: C 907 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8150 (t0) REVERT: H 4 LEU cc_start: 0.3233 (OUTLIER) cc_final: 0.2931 (pp) REVERT: H 96 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6218 (mtpm) REVERT: H 100 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.5226 (m-80) REVERT: I 47 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6116 (tm) outliers start: 158 outliers final: 105 residues processed: 365 average time/residue: 0.9269 time to fit residues: 417.8666 Evaluate side-chains 341 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 218 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 675 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 544 ASN B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 755 GLN C1005 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26951 Z= 0.341 Angle : 0.642 10.219 36684 Z= 0.339 Chirality : 0.050 0.593 4246 Planarity : 0.005 0.086 4678 Dihedral : 7.879 67.764 4244 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.39 % Rotamer: Outliers : 6.25 % Allowed : 20.71 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3269 helix: 1.46 (0.20), residues: 677 sheet: -0.32 (0.18), residues: 787 loop : -1.37 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.007 0.001 HIS B1101 PHE 0.024 0.002 PHE E 62 TYR 0.026 0.002 TYR C 453 ARG 0.003 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 219 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7074 (t0) REVERT: A 557 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7856 (mtmt) REVERT: A 564 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 755 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: A 994 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7816 (t70) REVERT: A 1073 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8199 (mtmm) REVERT: D 56 ASP cc_start: 0.6811 (m-30) cc_final: 0.6226 (m-30) REVERT: B 81 ASN cc_start: 0.7025 (p0) cc_final: 0.6508 (p0) REVERT: B 278 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8847 (ttpp) REVERT: B 321 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6189 (pm20) REVERT: B 333 THR cc_start: 0.5757 (OUTLIER) cc_final: 0.5488 (m) REVERT: B 390 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7898 (mt) REVERT: B 398 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: B 532 ASN cc_start: 0.6650 (t0) cc_final: 0.6383 (m-40) REVERT: C 96 GLU cc_start: 0.5499 (mm-30) cc_final: 0.4722 (mm-30) REVERT: C 234 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6518 (p0) REVERT: C 314 GLN cc_start: 0.8650 (mt0) cc_final: 0.8357 (mm-40) REVERT: C 324 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: C 516 GLU cc_start: 0.7174 (tt0) cc_final: 0.6911 (tt0) REVERT: C 907 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8237 (t0) REVERT: C 1092 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6668 (pp20) REVERT: H 4 LEU cc_start: 0.3302 (OUTLIER) cc_final: 0.2973 (pp) REVERT: H 36 TRP cc_start: 0.5073 (OUTLIER) cc_final: 0.4793 (m100) REVERT: H 100 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.5293 (m-80) REVERT: H 100 SER cc_start: 0.6122 (OUTLIER) cc_final: 0.5832 (t) REVERT: I 47 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6052 (tm) REVERT: I 88 CYS cc_start: 0.3892 (OUTLIER) cc_final: 0.1586 (p) outliers start: 177 outliers final: 116 residues processed: 367 average time/residue: 0.9600 time to fit residues: 435.7603 Evaluate side-chains 354 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 217 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 675 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 544 ASN B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN I 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26951 Z= 0.206 Angle : 0.574 9.418 36684 Z= 0.301 Chirality : 0.047 0.579 4246 Planarity : 0.005 0.082 4678 Dihedral : 7.328 66.601 4242 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.08 % Favored : 94.74 % Rotamer: Outliers : 5.30 % Allowed : 21.70 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3269 helix: 1.81 (0.20), residues: 664 sheet: -0.19 (0.18), residues: 762 loop : -1.29 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.004 0.001 HIS B1101 PHE 0.014 0.001 PHE B 643 TYR 0.024 0.001 TYR C 453 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 224 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7024 (t0) REVERT: A 557 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7860 (mtmt) REVERT: A 564 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: A 755 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: A 994 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7817 (t70) REVERT: D 56 ASP cc_start: 0.6778 (m-30) cc_final: 0.6162 (m-30) REVERT: B 81 ASN cc_start: 0.7055 (p0) cc_final: 0.6535 (p0) REVERT: B 278 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8785 (ttpp) REVERT: B 321 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6134 (pm20) REVERT: B 333 THR cc_start: 0.5661 (OUTLIER) cc_final: 0.5377 (m) REVERT: B 390 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7807 (mt) REVERT: B 398 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7085 (m-30) REVERT: B 429 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5518 (p90) REVERT: B 532 ASN cc_start: 0.6563 (t0) cc_final: 0.6305 (m-40) REVERT: B 811 LYS cc_start: 0.7130 (ptpt) cc_final: 0.6822 (mmtp) REVERT: C 169 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: C 234 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6541 (p0) REVERT: C 314 GLN cc_start: 0.8606 (mt0) cc_final: 0.8321 (mm-40) REVERT: C 516 GLU cc_start: 0.7089 (tt0) cc_final: 0.6839 (tt0) REVERT: C 658 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8069 (m-40) REVERT: C 907 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8148 (t0) REVERT: C 1092 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6504 (pp20) REVERT: H 4 LEU cc_start: 0.3420 (OUTLIER) cc_final: 0.3075 (pp) REVERT: H 36 TRP cc_start: 0.5024 (OUTLIER) cc_final: 0.4727 (m100) REVERT: H 96 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6185 (mtpm) REVERT: H 100 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.5113 (m-80) REVERT: I 47 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6034 (tm) REVERT: I 88 CYS cc_start: 0.4175 (OUTLIER) cc_final: 0.1765 (p) outliers start: 150 outliers final: 105 residues processed: 349 average time/residue: 0.9856 time to fit residues: 421.7783 Evaluate side-chains 341 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 214 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 87 TYR Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 675 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 544 ASN B 836 GLN B1101 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26951 Z= 0.226 Angle : 0.587 9.111 36684 Z= 0.308 Chirality : 0.047 0.601 4246 Planarity : 0.005 0.084 4678 Dihedral : 7.232 66.365 4238 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.75 % Favored : 94.07 % Rotamer: Outliers : 5.05 % Allowed : 22.16 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3269 helix: 1.80 (0.20), residues: 664 sheet: -0.17 (0.18), residues: 757 loop : -1.27 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.007 0.001 HIS B1101 PHE 0.016 0.001 PHE E 62 TYR 0.027 0.002 TYR A 170 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 218 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6992 (t0) REVERT: A 557 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7857 (mtmt) REVERT: A 564 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: A 755 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: A 994 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (t70) REVERT: D 56 ASP cc_start: 0.6795 (m-30) cc_final: 0.6175 (m-30) REVERT: B 81 ASN cc_start: 0.7061 (p0) cc_final: 0.6526 (p0) REVERT: B 278 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8827 (ttpp) REVERT: B 321 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6139 (pm20) REVERT: B 333 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5428 (m) REVERT: B 390 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7807 (mt) REVERT: B 398 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: B 532 ASN cc_start: 0.6577 (t0) cc_final: 0.6330 (m-40) REVERT: B 811 LYS cc_start: 0.7125 (ptpt) cc_final: 0.6812 (mmtp) REVERT: C 96 GLU cc_start: 0.5454 (mm-30) cc_final: 0.4719 (mm-30) REVERT: C 234 ASN cc_start: 0.7008 (OUTLIER) cc_final: 0.6554 (p0) REVERT: C 314 GLN cc_start: 0.8609 (mt0) cc_final: 0.8323 (mm-40) REVERT: C 516 GLU cc_start: 0.7088 (tt0) cc_final: 0.6824 (tt0) REVERT: C 658 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8046 (m-40) REVERT: C 907 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8162 (t0) REVERT: C 1092 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6589 (pp20) REVERT: H 4 LEU cc_start: 0.3440 (OUTLIER) cc_final: 0.3059 (pp) REVERT: H 36 TRP cc_start: 0.5106 (OUTLIER) cc_final: 0.4818 (m100) REVERT: H 96 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6179 (mtpm) REVERT: H 100 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: I 47 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.5965 (tm) REVERT: I 88 CYS cc_start: 0.4046 (OUTLIER) cc_final: 0.1685 (p) outliers start: 143 outliers final: 103 residues processed: 337 average time/residue: 0.9730 time to fit residues: 405.2364 Evaluate side-chains 341 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 218 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 87 TYR Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 0.5980 chunk 314 optimal weight: 10.0000 chunk 191 optimal weight: 0.0870 chunk 149 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 675 GLN A 935 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 544 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 321 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26951 Z= 0.227 Angle : 0.585 9.237 36684 Z= 0.308 Chirality : 0.047 0.612 4246 Planarity : 0.005 0.081 4678 Dihedral : 7.074 66.002 4234 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 4.70 % Allowed : 22.44 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3269 helix: 1.81 (0.20), residues: 664 sheet: -0.13 (0.18), residues: 758 loop : -1.25 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS B1064 PHE 0.015 0.001 PHE E 62 TYR 0.025 0.002 TYR A 170 ARG 0.004 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 222 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7024 (t0) REVERT: A 557 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7859 (mtmt) REVERT: A 564 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 755 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: A 994 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7815 (t70) REVERT: A 1073 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8186 (mtmm) REVERT: D 56 ASP cc_start: 0.6796 (m-30) cc_final: 0.6212 (m-30) REVERT: B 81 ASN cc_start: 0.7070 (p0) cc_final: 0.6559 (p0) REVERT: B 278 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8802 (ttpp) REVERT: B 321 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: B 333 THR cc_start: 0.5763 (OUTLIER) cc_final: 0.5466 (m) REVERT: B 390 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7766 (mt) REVERT: B 398 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: B 532 ASN cc_start: 0.6567 (t0) cc_final: 0.6309 (m-40) REVERT: B 745 ASP cc_start: 0.6844 (p0) cc_final: 0.6634 (p0) REVERT: B 811 LYS cc_start: 0.7132 (ptpt) cc_final: 0.6819 (mmtp) REVERT: C 96 GLU cc_start: 0.5485 (mm-30) cc_final: 0.4735 (mm-30) REVERT: C 234 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6561 (p0) REVERT: C 314 GLN cc_start: 0.8619 (mt0) cc_final: 0.8329 (mm-40) REVERT: C 324 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: C 516 GLU cc_start: 0.7108 (tt0) cc_final: 0.6854 (tt0) REVERT: C 658 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8058 (m-40) REVERT: C 907 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8185 (t0) REVERT: C 1092 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6606 (pp20) REVERT: H 4 LEU cc_start: 0.3455 (OUTLIER) cc_final: 0.3057 (pp) REVERT: H 36 TRP cc_start: 0.5089 (OUTLIER) cc_final: 0.4835 (m100) REVERT: H 96 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.6189 (mtpm) REVERT: H 100 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5147 (m-80) REVERT: I 47 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.5961 (tm) REVERT: I 88 CYS cc_start: 0.4059 (OUTLIER) cc_final: 0.1585 (p) outliers start: 133 outliers final: 98 residues processed: 332 average time/residue: 1.0071 time to fit residues: 415.2270 Evaluate side-chains 338 residues out of total 2932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 218 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 87 TYR Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 270 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN D 100FASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 544 ASN B1101 HIS C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.156168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112109 restraints weight = 32623.544| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.87 r_work: 0.3070 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26951 Z= 0.182 Angle : 0.557 8.460 36684 Z= 0.292 Chirality : 0.046 0.584 4246 Planarity : 0.005 0.083 4678 Dihedral : 6.725 65.250 4227 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 4.42 % Allowed : 22.61 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3269 helix: 1.88 (0.20), residues: 672 sheet: -0.06 (0.18), residues: 761 loop : -1.20 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.006 0.001 HIS B1101 PHE 0.014 0.001 PHE B 643 TYR 0.025 0.001 TYR A 170 ARG 0.004 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8545.96 seconds wall clock time: 154 minutes 20.83 seconds (9260.83 seconds total)