Starting phenix.real_space_refine on Mon Feb 19 19:35:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqu_34035/02_2024/7yqu_34035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqu_34035/02_2024/7yqu_34035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqu_34035/02_2024/7yqu_34035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqu_34035/02_2024/7yqu_34035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqu_34035/02_2024/7yqu_34035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqu_34035/02_2024/7yqu_34035.pdb" } resolution = 3.19 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= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16305 2.51 5 N 4209 2.21 5 O 4959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25587 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 13.26, per 1000 atoms: 0.52 Number of scatterers: 25587 At special positions: 0 Unit cell: (143.38, 151.94, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4959 8.00 N 4209 7.00 C 16305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 4.6 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 21.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.765A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.695A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 removed outlier: 3.884A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 817 through 822' Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP C 843 " --> pdb=" O CYS C 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 840 through 844' Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 869 through 880 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.638A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.699A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.765A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.694A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 819 Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 844' Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 869 through 880 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.638A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.699A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.766A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.694A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 removed outlier: 3.660A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP B 843 " --> pdb=" O CYS B 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 840 through 844' Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.637A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.698A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.953A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.537A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 107 removed outlier: 3.679A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.849A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.711A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.787A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.783A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.952A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.536A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.848A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.788A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.594A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.646A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.953A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 101 through 107 removed outlier: 3.679A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.849A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.788A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AE9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'B' and resid 1094 through 1097 802 hydrogen bonds defined for protein. 2193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.70 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4141 1.31 - 1.44: 7343 1.44 - 1.57: 14553 1.57 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 26178 Sorted by residual: bond pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta sigma weight residual 1.469 1.435 0.034 7.40e-03 1.83e+04 2.10e+01 bond pdb=" C PRO A 373 " pdb=" O PRO A 373 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C PRO B 373 " pdb=" O PRO B 373 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" CA ALA C 372 " pdb=" CB ALA C 372 " ideal model delta sigma weight residual 1.530 1.471 0.058 1.58e-02 4.01e+03 1.36e+01 bond pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 1.469 1.423 0.045 1.28e-02 6.10e+03 1.26e+01 ... (remaining 26173 not shown) Histogram of bond angle deviations from ideal: 89.57 - 98.46: 6 98.46 - 107.34: 913 107.34 - 116.23: 16777 116.23 - 125.12: 17618 125.12 - 134.01: 323 Bond angle restraints: 35637 Sorted by residual: angle pdb=" C PHE B 377 " pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " ideal model delta sigma weight residual 110.79 89.57 21.22 1.63e+00 3.76e-01 1.70e+02 angle pdb=" C PHE C 377 " pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta sigma weight residual 111.68 90.93 20.75 1.68e+00 3.54e-01 1.53e+02 angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 122.65 -8.85 1.00e+00 1.00e+00 7.83e+01 angle pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " pdb=" CG PHE C 377 " ideal model delta sigma weight residual 113.80 122.37 -8.57 1.00e+00 1.00e+00 7.34e+01 angle pdb=" C PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta sigma weight residual 109.80 97.27 12.53 1.64e+00 3.72e-01 5.84e+01 ... (remaining 35632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14602 17.99 - 35.99: 1300 35.99 - 53.98: 256 53.98 - 71.97: 33 71.97 - 89.97: 36 Dihedral angle restraints: 16227 sinusoidal: 6939 harmonic: 9288 Sorted by residual: dihedral pdb=" C PHE B 377 " pdb=" N PHE B 377 " pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " ideal model delta harmonic sigma weight residual -122.60 -97.22 -25.38 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" C PHE C 377 " pdb=" N PHE C 377 " pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta harmonic sigma weight residual -122.60 -99.91 -22.69 0 2.50e+00 1.60e-01 8.24e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 29.30 63.70 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 16224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3837 0.092 - 0.185: 321 0.185 - 0.277: 3 0.277 - 0.370: 3 0.370 - 0.462: 3 Chirality restraints: 4167 Sorted by residual: chirality pdb=" CA PHE B 377 " pdb=" N PHE B 377 " pdb=" C PHE B 377 " pdb=" CB PHE B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA PHE C 377 " pdb=" N PHE C 377 " pdb=" C PHE C 377 " pdb=" CB PHE C 377 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 4164 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 372 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ALA A 372 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA A 372 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 373 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 372 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ALA B 372 " 0.066 2.00e-02 2.50e+03 pdb=" O ALA B 372 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 373 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 818 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ILE C 818 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE C 818 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU C 819 " 0.022 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 7558 2.81 - 3.51: 30387 3.51 - 4.20: 53037 4.20 - 4.90: 99490 Nonbonded interactions: 190475 Sorted by model distance: nonbonded pdb=" NH2 ARG C 847 " pdb=" OD2 ASP A 568 " model vdw 1.425 2.520 nonbonded pdb=" NH2 ARG A 847 " pdb=" OD2 ASP B 568 " model vdw 1.443 2.520 nonbonded pdb=" OD2 ASP C 568 " pdb=" NH2 ARG B 847 " model vdw 1.445 2.520 nonbonded pdb=" CG1 VAL C1094 " pdb=" OH TYR B 904 " model vdw 2.160 3.460 nonbonded pdb=" OH TYR A 904 " pdb=" CG1 VAL B1094 " model vdw 2.180 3.460 ... (remaining 190470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 8.640 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 64.660 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26178 Z= 0.338 Angle : 0.716 21.223 35637 Z= 0.392 Chirality : 0.050 0.462 4167 Planarity : 0.004 0.042 4563 Dihedral : 14.037 89.966 10140 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.48 % Favored : 91.48 % Rotamer: Outliers : 0.14 % Allowed : 0.22 % Favored : 99.64 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3159 helix: 0.28 (0.22), residues: 609 sheet: 0.29 (0.20), residues: 630 loop : -1.95 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.003 0.001 HIS C1064 PHE 0.028 0.002 PHE A 906 TYR 0.047 0.002 TYR A 495 ARG 0.005 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 2.903 Fit side-chains REVERT: C 375 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 934 ILE cc_start: 0.9094 (tt) cc_final: 0.8893 (tt) REVERT: C 1050 MET cc_start: 0.8291 (mtp) cc_final: 0.8057 (mtp) REVERT: A 375 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: A 1138 TYR cc_start: 0.7551 (m-80) cc_final: 0.7269 (t80) REVERT: B 375 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 428 ASP cc_start: 0.7994 (p0) cc_final: 0.7749 (p0) REVERT: B 985 ASP cc_start: 0.8294 (p0) cc_final: 0.7995 (p0) REVERT: B 1072 GLU cc_start: 0.8106 (pm20) cc_final: 0.7783 (pm20) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.3604 time to fit residues: 122.4444 Evaluate side-chains 166 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0370 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN A 134 GLN A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26178 Z= 0.202 Angle : 0.567 9.473 35637 Z= 0.288 Chirality : 0.045 0.325 4167 Planarity : 0.004 0.066 4563 Dihedral : 6.340 57.349 4440 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.83 % Allowed : 6.53 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 3159 helix: 0.71 (0.22), residues: 615 sheet: 0.53 (0.20), residues: 660 loop : -1.98 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 PHE 0.014 0.001 PHE B 135 TYR 0.035 0.001 TYR A 495 ARG 0.003 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 2.792 Fit side-chains REVERT: C 375 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: A 574 ASP cc_start: 0.8265 (t0) cc_final: 0.8019 (t0) REVERT: A 1138 TYR cc_start: 0.7598 (m-80) cc_final: 0.7352 (t80) REVERT: B 375 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 377 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7049 (m-10) REVERT: B 1072 GLU cc_start: 0.8104 (pm20) cc_final: 0.7799 (pm20) outliers start: 23 outliers final: 16 residues processed: 178 average time/residue: 0.3517 time to fit residues: 102.0590 Evaluate side-chains 168 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 134 GLN B 207 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26178 Z= 0.339 Angle : 0.614 9.271 35637 Z= 0.313 Chirality : 0.047 0.331 4167 Planarity : 0.005 0.059 4563 Dihedral : 5.997 56.270 4440 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.55 % Allowed : 9.49 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3159 helix: 0.68 (0.22), residues: 612 sheet: 0.59 (0.20), residues: 648 loop : -2.08 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 633 HIS 0.005 0.001 HIS C1064 PHE 0.028 0.002 PHE C 906 TYR 0.043 0.002 TYR A 495 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 2.639 Fit side-chains REVERT: C 375 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: A 574 ASP cc_start: 0.8288 (t0) cc_final: 0.8024 (t0) REVERT: B 375 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: B 1072 GLU cc_start: 0.8165 (pm20) cc_final: 0.7839 (pm20) outliers start: 43 outliers final: 27 residues processed: 192 average time/residue: 0.3448 time to fit residues: 108.6971 Evaluate side-chains 177 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 275 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1125 ASN B 134 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26178 Z= 0.179 Angle : 0.533 9.321 35637 Z= 0.272 Chirality : 0.045 0.328 4167 Planarity : 0.004 0.054 4563 Dihedral : 5.425 56.739 4438 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.70 % Allowed : 11.26 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3159 helix: 0.88 (0.23), residues: 615 sheet: 0.65 (0.20), residues: 654 loop : -1.96 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.013 0.001 PHE B 906 TYR 0.023 0.001 TYR C 495 ARG 0.002 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 2.832 Fit side-chains REVERT: C 375 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: C 495 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.5747 (t80) REVERT: A 212 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.4047 (tp) REVERT: A 574 ASP cc_start: 0.8223 (t0) cc_final: 0.7813 (t0) REVERT: B 212 LEU cc_start: 0.4233 (OUTLIER) cc_final: 0.3990 (tp) REVERT: B 375 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: B 495 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6243 (t80) REVERT: B 1072 GLU cc_start: 0.8134 (pm20) cc_final: 0.7831 (pm20) outliers start: 47 outliers final: 30 residues processed: 206 average time/residue: 0.3484 time to fit residues: 118.0569 Evaluate side-chains 189 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL 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 B residue 66 HIS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.0980 chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1125 ASN B 134 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 26178 Z= 0.462 Angle : 0.664 9.355 35637 Z= 0.338 Chirality : 0.049 0.329 4167 Planarity : 0.005 0.053 4563 Dihedral : 5.645 56.098 4438 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.42 % Allowed : 12.91 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3159 helix: 0.60 (0.22), residues: 612 sheet: 0.50 (0.20), residues: 648 loop : -2.18 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 436 HIS 0.006 0.001 HIS C1064 PHE 0.027 0.002 PHE C 86 TYR 0.046 0.002 TYR C 495 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 161 time to evaluate : 2.954 Fit side-chains REVERT: C 375 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: C 433 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8474 (t) REVERT: C 495 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 176 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5650 (mt) REVERT: A 574 ASP cc_start: 0.8301 (t0) cc_final: 0.7830 (t0) REVERT: B 212 LEU cc_start: 0.4370 (OUTLIER) cc_final: 0.4101 (tp) REVERT: B 375 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: B 495 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6236 (t80) outliers start: 67 outliers final: 38 residues processed: 210 average time/residue: 0.3318 time to fit residues: 115.9407 Evaluate side-chains 199 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 chunk 255 optimal weight: 0.2980 chunk 142 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1125 ASN B 134 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26178 Z= 0.142 Angle : 0.522 9.253 35637 Z= 0.265 Chirality : 0.044 0.318 4167 Planarity : 0.004 0.050 4563 Dihedral : 5.076 56.952 4438 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.84 % Allowed : 14.68 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3159 helix: 0.95 (0.23), residues: 615 sheet: 0.63 (0.20), residues: 654 loop : -1.98 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.011 0.001 PHE A1121 TYR 0.021 0.001 TYR C 170 ARG 0.002 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 2.703 Fit side-chains REVERT: C 375 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: C 495 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6364 (t80) REVERT: A 212 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4090 (tp) REVERT: A 574 ASP cc_start: 0.8140 (t0) cc_final: 0.7770 (t0) REVERT: B 212 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.4021 (tp) REVERT: B 375 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: B 495 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6084 (t80) outliers start: 51 outliers final: 31 residues processed: 209 average time/residue: 0.3303 time to fit residues: 115.7528 Evaluate side-chains 192 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26178 Z= 0.345 Angle : 0.607 9.349 35637 Z= 0.308 Chirality : 0.047 0.323 4167 Planarity : 0.004 0.048 4563 Dihedral : 5.249 56.151 4438 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.34 % Allowed : 14.86 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3159 helix: 0.84 (0.22), residues: 612 sheet: 0.58 (0.20), residues: 648 loop : -2.09 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 633 HIS 0.004 0.001 HIS C1064 PHE 0.021 0.002 PHE C 86 TYR 0.040 0.002 TYR C 495 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 157 time to evaluate : 4.237 Fit side-chains REVERT: C 375 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: C 495 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6153 (t80) REVERT: C 787 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: A 212 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4089 (tp) REVERT: A 303 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7636 (pp) REVERT: A 433 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (t) REVERT: A 574 ASP cc_start: 0.8238 (t0) cc_final: 0.7829 (t0) REVERT: A 629 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7372 (tt) REVERT: B 212 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4081 (tp) REVERT: B 375 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: B 495 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6132 (t80) outliers start: 65 outliers final: 44 residues processed: 209 average time/residue: 0.3517 time to fit residues: 122.2386 Evaluate side-chains 203 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 149 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 151 optimal weight: 0.0270 chunk 28 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 134 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26178 Z= 0.139 Angle : 0.516 9.235 35637 Z= 0.262 Chirality : 0.044 0.318 4167 Planarity : 0.004 0.056 4563 Dihedral : 4.878 56.747 4438 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.80 % Allowed : 15.62 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3159 helix: 1.05 (0.23), residues: 615 sheet: 0.73 (0.21), residues: 582 loop : -1.89 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.013 0.001 PHE A 135 TYR 0.020 0.001 TYR C 495 ARG 0.002 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 2.893 Fit side-chains revert: symmetry clash REVERT: C 375 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: C 495 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6406 (t80) REVERT: C 787 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: A 212 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.4000 (tp) REVERT: A 574 ASP cc_start: 0.8163 (t0) cc_final: 0.7775 (t0) REVERT: B 212 LEU cc_start: 0.4222 (OUTLIER) cc_final: 0.3995 (tp) REVERT: B 495 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.5885 (t80) REVERT: B 1072 GLU cc_start: 0.8120 (pm20) cc_final: 0.7846 (pm20) outliers start: 50 outliers final: 40 residues processed: 212 average time/residue: 0.3327 time to fit residues: 117.2675 Evaluate side-chains 207 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 161 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 26178 Z= 0.302 Angle : 0.587 10.628 35637 Z= 0.297 Chirality : 0.047 0.322 4167 Planarity : 0.004 0.054 4563 Dihedral : 5.001 56.197 4436 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.16 % Allowed : 15.30 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3159 helix: 0.97 (0.23), residues: 612 sheet: 0.59 (0.20), residues: 654 loop : -2.01 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.004 0.001 HIS C1064 PHE 0.020 0.001 PHE C 86 TYR 0.037 0.001 TYR C 495 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 151 time to evaluate : 3.114 Fit side-chains REVERT: C 375 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: C 433 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8564 (t) REVERT: C 495 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6167 (t80) REVERT: C 787 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: A 212 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4069 (tp) REVERT: A 433 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8508 (t) REVERT: A 574 ASP cc_start: 0.8186 (t0) cc_final: 0.7802 (t0) REVERT: A 629 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7304 (tt) REVERT: B 212 LEU cc_start: 0.4289 (OUTLIER) cc_final: 0.4045 (tp) REVERT: B 375 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: B 495 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6073 (t80) REVERT: B 1072 GLU cc_start: 0.8193 (pm20) cc_final: 0.7908 (pm20) outliers start: 60 outliers final: 46 residues processed: 201 average time/residue: 0.3302 time to fit residues: 111.9860 Evaluate side-chains 206 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 150 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 209 optimal weight: 0.0970 chunk 316 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 0.0000 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.002 0.031 26178 Z= 0.129 Angle : 0.509 9.620 35637 Z= 0.256 Chirality : 0.044 0.315 4167 Planarity : 0.004 0.055 4563 Dihedral : 4.641 56.848 4436 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.70 % Allowed : 15.87 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3159 helix: 1.08 (0.23), residues: 621 sheet: 0.61 (0.22), residues: 552 loop : -1.78 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.000 HIS A 207 PHE 0.015 0.001 PHE B 135 TYR 0.020 0.001 TYR A1138 ARG 0.002 0.000 ARG A 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 173 time to evaluate : 2.912 Fit side-chains revert: symmetry clash REVERT: C 375 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: C 495 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.6291 (t80) REVERT: C 787 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: C 902 MET cc_start: 0.8715 (tpp) cc_final: 0.8186 (mmm) REVERT: A 212 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3953 (tp) REVERT: A 433 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8452 (t) REVERT: A 529 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7380 (mmtp) REVERT: A 574 ASP cc_start: 0.8079 (t0) cc_final: 0.7709 (t0) REVERT: B 212 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4172 (tp) REVERT: B 495 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.5875 (t80) REVERT: B 1072 GLU cc_start: 0.8129 (pm20) cc_final: 0.7891 (pm20) outliers start: 47 outliers final: 37 residues processed: 212 average time/residue: 0.3403 time to fit residues: 120.7234 Evaluate side-chains 209 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093238 restraints weight = 35475.187| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.81 r_work: 0.2910 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26178 Z= 0.246 Angle : 0.554 9.875 35637 Z= 0.279 Chirality : 0.046 0.318 4167 Planarity : 0.004 0.053 4563 Dihedral : 4.765 56.304 4436 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.84 % Allowed : 15.95 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3159 helix: 1.09 (0.23), residues: 615 sheet: 0.67 (0.21), residues: 654 loop : -1.92 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 436 HIS 0.004 0.001 HIS A 207 PHE 0.017 0.001 PHE A 135 TYR 0.031 0.001 TYR C 495 ARG 0.004 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.89 seconds wall clock time: 81 minutes 2.52 seconds (4862.52 seconds total)