Starting phenix.real_space_refine on Wed Mar 20 18:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqz_34040/03_2024/7yqz_34040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqz_34040/03_2024/7yqz_34040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqz_34040/03_2024/7yqz_34040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqz_34040/03_2024/7yqz_34040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqz_34040/03_2024/7yqz_34040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqz_34040/03_2024/7yqz_34040.pdb" } resolution = 3.84 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= -0.001 sd= 0.051 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 123 5.16 5 C 17981 2.51 5 N 4662 2.21 5 O 5500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28266 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7986 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 966} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 55, 'TRANS': 969} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 7991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7991 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 55, 'TRANS': 966} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 15.07, per 1000 atoms: 0.53 Number of scatterers: 28266 At special positions: 0 Unit cell: (173.34, 157.29, 182.97, 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 123 16.00 O 5500 8.00 N 4662 7.00 C 17981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " 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 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B 801 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " 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 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C 801 " " NAG C1313 " - " ASN C1074 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG D 1 " - " ASN C 343 " " NAG E 1 " - " ASN A 343 " Time building additional restraints: 10.92 Conformation dependent library (CDL) restraints added in 5.0 seconds 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6566 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 55 sheets defined 18.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.761A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.903A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.231A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.506A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.780A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 778 removed outlier: 3.797A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.518A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 881 removed outlier: 3.844A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 903 removed outlier: 4.250A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 918 No H-bonds generated for 'chain 'C' and resid 916 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.577A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.595A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.665A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.596A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.786A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.241A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 755 removed outlier: 3.886A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 781 removed outlier: 3.580A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.131A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.695A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.549A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 4.347A pdb=" N MET A 902 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 903 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN A 907 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 908 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 910 " --> pdb=" O ASN A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.489A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.804A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.704A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.666A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.777A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.976A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.727A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.517A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 868 through 884 removed outlier: 4.020A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.045A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 903 Processing helix chain 'B' and resid 904 through 909 removed outlier: 4.508A pdb=" N ASN B 907 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 908 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.144A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.861A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.873A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.631A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.670A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.260A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.007A pdb=" N GLN J 65 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.597A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.158A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.589A 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 Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.503A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 326 removed outlier: 6.771A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 355 removed outlier: 4.324A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.881A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.777A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.622A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.558A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.482A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS A 187 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 210 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 51 through 55 removed outlier: 3.582A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 168 through 172 removed outlier: 3.887A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 312 through 319 removed outlier: 7.310A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.695A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.502A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.739A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.566A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.656A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.656A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.564A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.516A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.652A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AD6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.834A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.868A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.642A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 379 through 380 removed outlier: 3.675A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.340A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.340A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.565A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.682A pdb=" N VAL B1104 " --> pdb=" O GLN B1113 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'I' and resid 49 through 51 removed outlier: 4.563A pdb=" N ASN I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 49 through 51 Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AF3, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.978A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.602A pdb=" N ARG G 46 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 49 through 51 removed outlier: 4.170A pdb=" N ASN J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 49 through 51 Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.935A pdb=" N CYS H 23 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AG1, first strand: chain 'H' and resid 35 through 39 811 hydrogen bonds defined for protein. 2142 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: 11.04 Time building geometry restraints manager: 11.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 4015 1.25 - 1.40: 7773 1.40 - 1.55: 16886 1.55 - 1.70: 82 1.70 - 1.85: 156 Bond restraints: 28912 Sorted by residual: bond pdb=" CG PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 1.503 1.095 0.408 3.40e-02 8.65e+02 1.44e+02 bond pdb=" N PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.70e+01 bond pdb=" N ILE B 818 " pdb=" CA ILE B 818 " ideal model delta sigma weight residual 1.462 1.501 -0.039 1.06e-02 8.90e+03 1.37e+01 bond pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.91e+00 bond pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.31e-02 5.83e+03 9.41e+00 ... (remaining 28907 not shown) Histogram of bond angle deviations from ideal: 82.00 - 92.60: 2 92.60 - 103.20: 220 103.20 - 113.80: 16596 113.80 - 124.40: 21959 124.40 - 135.00: 557 Bond angle restraints: 39334 Sorted by residual: angle pdb=" N PRO C1079 " pdb=" CD PRO C1079 " pdb=" CG PRO C1079 " ideal model delta sigma weight residual 103.20 82.00 21.20 1.50e+00 4.44e-01 2.00e+02 angle pdb=" CA PRO C1079 " pdb=" N PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 112.00 96.64 15.36 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO C1079 " pdb=" CB PRO C1079 " pdb=" CG PRO C1079 " ideal model delta sigma weight residual 104.50 89.56 14.94 1.90e+00 2.77e-01 6.19e+01 angle pdb=" N GLU B 819 " pdb=" CA GLU B 819 " pdb=" C GLU B 819 " ideal model delta sigma weight residual 113.50 104.14 9.36 1.23e+00 6.61e-01 5.79e+01 angle pdb=" CA ARG I 85 " pdb=" CB ARG I 85 " pdb=" CG ARG I 85 " ideal model delta sigma weight residual 114.10 124.93 -10.83 2.00e+00 2.50e-01 2.93e+01 ... (remaining 39329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 16483 21.52 - 43.04: 1182 43.04 - 64.56: 139 64.56 - 86.08: 58 86.08 - 107.60: 15 Dihedral angle restraints: 17877 sinusoidal: 7641 harmonic: 10236 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 3.96 89.04 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 6.30 86.70 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.31 -85.69 1 1.00e+01 1.00e-02 8.88e+01 ... (remaining 17874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3853 0.071 - 0.142: 668 0.142 - 0.213: 44 0.213 - 0.284: 13 0.284 - 0.355: 4 Chirality restraints: 4582 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.17 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 4579 not shown) Planarity restraints: 5068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.107 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C1079 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP I 47 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TRP I 47 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP I 47 " 0.022 2.00e-02 2.50e+03 pdb=" N MET I 48 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 817 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C PRO B 817 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO B 817 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 818 " -0.018 2.00e-02 2.50e+03 ... (remaining 5065 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 14 2.28 - 2.94: 12341 2.94 - 3.59: 37469 3.59 - 4.25: 59949 4.25 - 4.90: 99603 Nonbonded interactions: 209376 Sorted by model distance: nonbonded pdb=" CG GLU B 96 " pdb=" CD1 ILE B 100 " model vdw 1.625 3.860 nonbonded pdb=" OE2 GLU B 96 " pdb=" CG1 ILE B 100 " model vdw 1.927 3.440 nonbonded pdb=" CD GLU B 96 " pdb=" CG1 ILE B 100 " model vdw 1.994 3.670 nonbonded pdb=" CG GLU B 96 " pdb=" CG1 ILE B 100 " model vdw 2.048 3.840 nonbonded pdb=" CG2 ILE A 100 " pdb=" CD2 LEU A 242 " model vdw 2.074 3.880 ... (remaining 209371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 263 or resid 265 through 622 or \ resid 641 through 826 or resid 854 through 1144 or resid 1301 through 1315)) selection = (chain 'B' and (resid 25 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 243 or resid 263 or resid 265 th \ rough 826 or resid 854 through 1144 or resid 1301 through 1315)) selection = (chain 'C' and (resid 25 through 622 or resid 641 through 826 or resid 854 throu \ gh 1144 or resid 1301 through 1315)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 11.410 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 73.450 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.408 28912 Z= 0.334 Angle : 0.804 21.205 39334 Z= 0.417 Chirality : 0.053 0.355 4582 Planarity : 0.006 0.147 5021 Dihedral : 14.509 107.605 11182 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.84 % Favored : 92.90 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.13), residues: 3481 helix: -2.56 (0.15), residues: 576 sheet: -0.74 (0.20), residues: 731 loop : -2.19 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 47 HIS 0.006 0.001 HIS A1048 PHE 0.045 0.002 PHE B 133 TYR 0.022 0.001 TYR B 265 ARG 0.007 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 250 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7606 (mpp80) REVERT: A 983 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8538 (ptp90) REVERT: A 1129 VAL cc_start: 0.9113 (m) cc_final: 0.8843 (p) REVERT: B 867 ASP cc_start: 0.8174 (p0) cc_final: 0.7778 (p0) REVERT: B 1002 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8481 (tp-100) REVERT: G 55 ARG cc_start: 0.4435 (mmm160) cc_final: 0.4214 (mmm-85) REVERT: J 4 LEU cc_start: 0.8075 (mt) cc_final: 0.7862 (mt) REVERT: H 96 LEU cc_start: 0.8021 (tp) cc_final: 0.7768 (tp) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.3714 time to fit residues: 152.2351 Evaluate side-chains 168 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1011 GLN A1125 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN G 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28912 Z= 0.181 Angle : 0.591 10.874 39334 Z= 0.298 Chirality : 0.044 0.271 4582 Planarity : 0.004 0.058 5021 Dihedral : 7.494 66.994 4901 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.49 % Allowed : 7.76 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.13), residues: 3481 helix: -0.73 (0.20), residues: 597 sheet: -0.65 (0.21), residues: 695 loop : -2.07 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 47 HIS 0.006 0.001 HIS C 505 PHE 0.016 0.001 PHE A 392 TYR 0.024 0.001 TYR C 453 ARG 0.005 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8763 (m-30) cc_final: 0.8384 (m-30) REVERT: B 867 ASP cc_start: 0.8212 (p0) cc_final: 0.7795 (p0) REVERT: I 48 MET cc_start: 0.6732 (mmm) cc_final: 0.6487 (mmm) REVERT: J 29 PHE cc_start: 0.8312 (t80) cc_final: 0.8025 (t80) REVERT: H 98 PHE cc_start: 0.7545 (m-10) cc_final: 0.7344 (m-10) outliers start: 15 outliers final: 13 residues processed: 208 average time/residue: 0.3713 time to fit residues: 129.9008 Evaluate side-chains 178 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 264 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 315 optimal weight: 40.0000 chunk 108 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 185 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28912 Z= 0.236 Angle : 0.585 11.377 39334 Z= 0.294 Chirality : 0.044 0.250 4582 Planarity : 0.004 0.053 5021 Dihedral : 6.567 59.299 4901 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.82 % Allowed : 11.81 % Favored : 87.37 % 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: -1.92 (0.14), residues: 3481 helix: 0.04 (0.22), residues: 597 sheet: -0.67 (0.20), residues: 719 loop : -1.97 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 47 HIS 0.006 0.001 HIS A 66 PHE 0.029 0.001 PHE C 55 TYR 0.027 0.001 TYR A 265 ARG 0.006 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.7944 (m-80) cc_final: 0.7727 (m-80) REVERT: B 133 PHE cc_start: 0.7340 (m-80) cc_final: 0.6507 (p90) REVERT: B 867 ASP cc_start: 0.8443 (p0) cc_final: 0.7954 (p0) REVERT: I 48 MET cc_start: 0.6701 (mmm) cc_final: 0.6470 (mmm) REVERT: I 54 TYR cc_start: 0.8465 (t80) cc_final: 0.8131 (t80) REVERT: J 80 TYR cc_start: 0.6673 (m-80) cc_final: 0.6351 (m-10) outliers start: 25 outliers final: 16 residues processed: 196 average time/residue: 0.3653 time to fit residues: 120.8500 Evaluate side-chains 178 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 30.0000 chunk 239 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 439 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1125 ASN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN G 92 HIS ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28912 Z= 0.273 Angle : 0.593 9.377 39334 Z= 0.300 Chirality : 0.045 0.244 4582 Planarity : 0.004 0.049 5021 Dihedral : 6.237 59.649 4901 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.57 % Allowed : 13.65 % Favored : 84.78 % 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: -1.90 (0.14), residues: 3481 helix: 0.16 (0.22), residues: 600 sheet: -0.72 (0.20), residues: 725 loop : -1.97 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 47 HIS 0.004 0.001 HIS A 49 PHE 0.020 0.001 PHE H 98 TYR 0.022 0.001 TYR A 508 ARG 0.004 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 581 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8686 (p) REVERT: B 133 PHE cc_start: 0.7112 (m-80) cc_final: 0.6487 (p90) REVERT: I 48 MET cc_start: 0.6717 (mmm) cc_final: 0.6485 (mmm) outliers start: 48 outliers final: 30 residues processed: 203 average time/residue: 0.3709 time to fit residues: 126.7739 Evaluate side-chains 185 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 288 optimal weight: 0.2980 chunk 233 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 303 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28912 Z= 0.334 Angle : 0.632 12.234 39334 Z= 0.319 Chirality : 0.045 0.243 4582 Planarity : 0.004 0.050 5021 Dihedral : 6.264 59.590 4901 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.87 % Allowed : 15.58 % Favored : 82.56 % 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: -1.99 (0.14), residues: 3481 helix: 0.11 (0.22), residues: 601 sheet: -0.80 (0.20), residues: 720 loop : -2.03 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 47 HIS 0.005 0.001 HIS C 505 PHE 0.042 0.002 PHE J 29 TYR 0.021 0.002 TYR A1067 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 161 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8839 (p) REVERT: C 581 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8671 (p) REVERT: A 1122 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7835 (p) REVERT: B 133 PHE cc_start: 0.7062 (m-80) cc_final: 0.6641 (p90) REVERT: B 900 MET cc_start: 0.7328 (mmm) cc_final: 0.6658 (mmm) REVERT: I 48 MET cc_start: 0.6825 (mmm) cc_final: 0.6583 (mmm) REVERT: G 37 TYR cc_start: 0.5509 (m-80) cc_final: 0.5142 (m-80) outliers start: 57 outliers final: 35 residues processed: 204 average time/residue: 0.3875 time to fit residues: 132.8018 Evaluate side-chains 191 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 0.0470 chunk 177 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 774 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28912 Z= 0.144 Angle : 0.551 11.728 39334 Z= 0.274 Chirality : 0.044 0.239 4582 Planarity : 0.004 0.048 5021 Dihedral : 5.720 59.988 4901 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.47 % Allowed : 16.79 % Favored : 81.74 % 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: -1.73 (0.14), residues: 3481 helix: 0.55 (0.22), residues: 603 sheet: -0.66 (0.21), residues: 697 loop : -1.91 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 50 HIS 0.006 0.001 HIS A 49 PHE 0.036 0.001 PHE J 29 TYR 0.014 0.001 TYR A1067 ARG 0.006 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8842 (p) REVERT: C 727 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8729 (mm) REVERT: A 1122 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7693 (p) REVERT: B 133 PHE cc_start: 0.6986 (m-80) cc_final: 0.6752 (p90) REVERT: B 867 ASP cc_start: 0.8433 (p0) cc_final: 0.7963 (p0) REVERT: B 900 MET cc_start: 0.7097 (mmm) cc_final: 0.6434 (mmm) REVERT: I 48 MET cc_start: 0.6755 (mmm) cc_final: 0.6530 (mmm) REVERT: G 55 ARG cc_start: 0.4229 (mmt-90) cc_final: 0.3035 (tpp-160) outliers start: 45 outliers final: 32 residues processed: 210 average time/residue: 0.3646 time to fit residues: 128.6455 Evaluate side-chains 197 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 285 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 337 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 28912 Z= 0.352 Angle : 0.662 11.439 39334 Z= 0.334 Chirality : 0.046 0.249 4582 Planarity : 0.004 0.049 5021 Dihedral : 6.090 59.365 4901 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.23 % Allowed : 17.21 % Favored : 80.56 % 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: -1.98 (0.14), residues: 3481 helix: 0.26 (0.22), residues: 599 sheet: -0.88 (0.20), residues: 733 loop : -2.04 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 47 HIS 0.004 0.001 HIS B1064 PHE 0.046 0.002 PHE J 29 TYR 0.019 0.002 TYR A1067 ARG 0.008 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 162 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8350 (tp) cc_final: 0.8122 (tt) REVERT: C 236 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8829 (p) REVERT: C 546 LEU cc_start: 0.9311 (tt) cc_final: 0.8868 (tt) REVERT: A 1122 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 133 PHE cc_start: 0.7104 (m-80) cc_final: 0.6766 (p90) REVERT: B 900 MET cc_start: 0.7387 (mmm) cc_final: 0.6780 (mmm) REVERT: I 48 MET cc_start: 0.6755 (mmm) cc_final: 0.6512 (mmm) REVERT: G 37 TYR cc_start: 0.5610 (m-80) cc_final: 0.5175 (m-80) REVERT: G 55 ARG cc_start: 0.4504 (mmt-90) cc_final: 0.3340 (tpp-160) outliers start: 68 outliers final: 48 residues processed: 216 average time/residue: 0.3660 time to fit residues: 133.7723 Evaluate side-chains 201 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain I residue 55 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28912 Z= 0.160 Angle : 0.568 12.354 39334 Z= 0.283 Chirality : 0.044 0.243 4582 Planarity : 0.004 0.047 5021 Dihedral : 5.625 59.711 4901 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.34 % Allowed : 18.29 % Favored : 80.37 % 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: -1.70 (0.14), residues: 3481 helix: 0.71 (0.22), residues: 595 sheet: -0.71 (0.21), residues: 703 loop : -1.90 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 50 HIS 0.004 0.001 HIS A 49 PHE 0.049 0.001 PHE J 29 TYR 0.015 0.001 TYR A1067 ARG 0.005 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 546 LEU cc_start: 0.9257 (tt) cc_final: 0.8798 (tt) REVERT: A 117 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 175 PHE cc_start: 0.8128 (m-80) cc_final: 0.7918 (m-80) REVERT: A 1122 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 133 PHE cc_start: 0.7062 (m-80) cc_final: 0.6815 (p90) REVERT: B 731 MET cc_start: 0.8858 (ptp) cc_final: 0.8607 (ptm) REVERT: B 867 ASP cc_start: 0.8435 (p0) cc_final: 0.7893 (p0) REVERT: B 900 MET cc_start: 0.7233 (mmm) cc_final: 0.6667 (mmm) REVERT: I 48 MET cc_start: 0.6622 (mmm) cc_final: 0.6399 (mmm) outliers start: 41 outliers final: 33 residues processed: 205 average time/residue: 0.3779 time to fit residues: 129.0129 Evaluate side-chains 197 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 0.2980 chunk 323 optimal weight: 20.0000 chunk 294 optimal weight: 4.9990 chunk 314 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 40.0000 chunk 96 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 313 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28912 Z= 0.273 Angle : 0.612 12.248 39334 Z= 0.306 Chirality : 0.045 0.243 4582 Planarity : 0.004 0.044 5021 Dihedral : 5.724 59.519 4901 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.64 % Allowed : 18.72 % Favored : 79.65 % 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: -1.81 (0.14), residues: 3481 helix: 0.55 (0.22), residues: 600 sheet: -0.75 (0.21), residues: 696 loop : -1.97 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 50 HIS 0.003 0.001 HIS A 49 PHE 0.052 0.002 PHE J 29 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8362 (tp) cc_final: 0.8151 (tt) REVERT: C 236 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8823 (p) REVERT: C 546 LEU cc_start: 0.9300 (tt) cc_final: 0.8838 (tt) REVERT: A 117 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 1122 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7774 (p) REVERT: B 133 PHE cc_start: 0.7106 (m-80) cc_final: 0.6789 (p90) REVERT: B 900 MET cc_start: 0.7394 (mmm) cc_final: 0.6761 (mmm) REVERT: I 48 MET cc_start: 0.6655 (mmm) cc_final: 0.6425 (mmm) REVERT: G 37 TYR cc_start: 0.5374 (m-80) cc_final: 0.4898 (m-80) outliers start: 50 outliers final: 43 residues processed: 196 average time/residue: 0.3672 time to fit residues: 119.8867 Evaluate side-chains 204 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 0.5980 chunk 332 optimal weight: 0.5980 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 348 optimal weight: 3.9990 chunk 320 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 170 optimal weight: 0.0370 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28912 Z= 0.211 Angle : 0.590 12.572 39334 Z= 0.294 Chirality : 0.044 0.246 4582 Planarity : 0.004 0.045 5021 Dihedral : 5.617 59.826 4901 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.57 % Allowed : 18.78 % Favored : 79.65 % 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: -1.74 (0.14), residues: 3481 helix: 0.68 (0.22), residues: 597 sheet: -0.72 (0.21), residues: 696 loop : -1.93 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 50 HIS 0.003 0.001 HIS C 505 PHE 0.050 0.001 PHE J 29 TYR 0.017 0.001 TYR C 904 ARG 0.004 0.000 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8315 (tp) cc_final: 0.8091 (tt) REVERT: C 191 GLU cc_start: 0.8481 (tp30) cc_final: 0.8100 (mm-30) REVERT: C 236 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8836 (p) REVERT: C 546 LEU cc_start: 0.9289 (tt) cc_final: 0.8834 (tt) REVERT: A 117 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8722 (pp) REVERT: A 175 PHE cc_start: 0.8157 (m-80) cc_final: 0.7926 (m-80) REVERT: A 1122 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7767 (p) REVERT: B 731 MET cc_start: 0.8830 (ptp) cc_final: 0.8579 (ptm) REVERT: B 867 ASP cc_start: 0.8406 (p0) cc_final: 0.7911 (p0) REVERT: B 900 MET cc_start: 0.7275 (mmm) cc_final: 0.6697 (mmm) REVERT: I 48 MET cc_start: 0.6695 (mmm) cc_final: 0.6472 (mmm) REVERT: J 29 PHE cc_start: 0.8598 (t80) cc_final: 0.8058 (t80) outliers start: 48 outliers final: 44 residues processed: 198 average time/residue: 0.3573 time to fit residues: 118.1690 Evaluate side-chains 208 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 278 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 285 optimal weight: 0.9980 chunk 35 optimal weight: 0.0370 chunk 51 optimal weight: 7.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.106599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075293 restraints weight = 92042.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.077367 restraints weight = 58931.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077532 restraints weight = 36469.092| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28912 Z= 0.142 Angle : 0.559 12.807 39334 Z= 0.276 Chirality : 0.044 0.243 4582 Planarity : 0.004 0.047 5021 Dihedral : 5.246 59.633 4901 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.44 % Allowed : 18.82 % Favored : 79.74 % 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: -1.53 (0.14), residues: 3481 helix: 0.95 (0.23), residues: 593 sheet: -0.59 (0.21), residues: 702 loop : -1.82 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 50 HIS 0.004 0.001 HIS A1048 PHE 0.048 0.001 PHE J 29 TYR 0.013 0.001 TYR C 904 ARG 0.004 0.000 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.68 seconds wall clock time: 81 minutes 26.56 seconds (4886.56 seconds total)