Starting phenix.real_space_refine on Sun Apr 14 12:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wti_32787/04_2024/7wti_32787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wti_32787/04_2024/7wti_32787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wti_32787/04_2024/7wti_32787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wti_32787/04_2024/7wti_32787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wti_32787/04_2024/7wti_32787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wti_32787/04_2024/7wti_32787.pdb" } resolution = 3.8 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= -0.002 sd= 0.064 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 141 5.16 5 C 20127 2.51 5 N 5193 2.21 5 O 6075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 992": "OE1" <-> "OE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31536 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8623 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8623 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 61, 'TRANS': 1035} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8623 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 16.52, per 1000 atoms: 0.52 Number of scatterers: 31536 At special positions: 0 Unit cell: (162.64, 172.27, 231.12, 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 141 16.00 O 6075 8.00 N 5193 7.00 C 20127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 434 " distance=2.04 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 651 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 673 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 751 " distance=2.03 Simple disulfide: pdb=" SG CYS A1034 " - pdb=" SG CYS A1045 " distance=2.04 Simple disulfide: pdb=" SG CYS A1084 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 303 " distance=2.04 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 434 " distance=2.04 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 651 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B1034 " - pdb=" SG CYS B1045 " distance=2.03 Simple disulfide: pdb=" SG CYS B1084 " - pdb=" SG CYS B1128 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 527 " distance=2.04 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 651 " distance=2.03 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C1034 " - pdb=" SG CYS C1045 " distance=2.04 Simple disulfide: pdb=" SG CYS C1084 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 233 " " NAG A1303 " - " ASN A 284 " " NAG A1304 " - " ASN A 333 " " NAG A1305 " - " ASN A 345 " " NAG A1306 " - " ASN A 618 " " NAG A1307 " - " ASN A 711 " " NAG A1308 " - " ASN A 719 " " NAG A1309 " - " ASN A 803 " " NAG A1310 " - " ASN A1076 " " NAG A1311 " - " ASN A1100 " " NAG A1312 " - " ASN A1136 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 233 " " NAG B1303 " - " ASN B 284 " " NAG B1304 " - " ASN B 333 " " NAG B1305 " - " ASN B 345 " " NAG B1306 " - " ASN B 618 " " NAG B1307 " - " ASN B 711 " " NAG B1308 " - " ASN B 719 " " NAG B1309 " - " ASN B 803 " " NAG B1310 " - " ASN B1076 " " NAG B1311 " - " ASN B1100 " " NAG B1312 " - " ASN B1136 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 233 " " NAG C1303 " - " ASN C 284 " " NAG C1304 " - " ASN C 333 " " NAG C1305 " - " ASN C 345 " " NAG C1306 " - " ASN C 618 " " NAG C1307 " - " ASN C 711 " " NAG C1308 " - " ASN C 719 " " NAG C1309 " - " ASN C 803 " " NAG C1310 " - " ASN C1076 " " NAG C1311 " - " ASN C1100 " " NAG C1312 " - " ASN C1136 " Time building additional restraints: 12.59 Conformation dependent library (CDL) restraints added in 5.7 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7434 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 62 sheets defined 18.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.854A pdb=" N VAL A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 344' Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.646A pdb=" N LEU A 389 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 391 " --> pdb=" O LYS A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 391' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.057A pdb=" N GLU A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 409 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.861A pdb=" N TYR A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 744 " --> pdb=" O CYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 751 through 757 removed outlier: 3.766A pdb=" N GLN A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.900A pdb=" N GLN A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 828 removed outlier: 3.751A pdb=" N ASN A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 827 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 886 removed outlier: 3.591A pdb=" N ILE A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 873 " --> pdb=" O ASP A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.612A pdb=" N GLY A 891 " --> pdb=" O TRP A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'A' and resid 921 through 943 removed outlier: 3.810A pdb=" N GLN A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 929 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 937 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 970 removed outlier: 3.838A pdb=" N ASP A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 965 " --> pdb=" O LEU A 961 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 966 " --> pdb=" O ASN A 962 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 969 " --> pdb=" O VAL A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 986 Processing helix chain 'A' and resid 987 through 990 Processing helix chain 'A' and resid 991 through 1034 removed outlier: 5.088A pdb=" N ARG A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1120 No H-bonds generated for 'chain 'A' and resid 1118 through 1120' Processing helix chain 'A' and resid 1143 through 1163 removed outlier: 4.118A pdb=" N LEU A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A1152 " --> pdb=" O ASP A1148 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 339 through 345 removed outlier: 3.884A pdb=" N VAL B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.650A pdb=" N ASN B 372 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.989A pdb=" N GLU B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 409 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 410 " --> pdb=" O ASP B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.962A pdb=" N SER B 639 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 640 " --> pdb=" O VAL B 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 640' Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 750 through 757 removed outlier: 3.531A pdb=" N LEU B 754 " --> pdb=" O GLU B 750 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B 757 " --> pdb=" O ASN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 785 removed outlier: 3.599A pdb=" N GLY B 771 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 828 removed outlier: 3.523A pdb=" N LEU B 824 " --> pdb=" O ILE B 820 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 888 through 892 removed outlier: 3.670A pdb=" N GLY B 891 " --> pdb=" O TRP B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 removed outlier: 3.814A pdb=" N MET B 904 " --> pdb=" O PHE B 900 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN B 909 " --> pdb=" O ALA B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 4.364A pdb=" N TYR B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 915 through 920' Processing helix chain 'B' and resid 921 through 943 removed outlier: 3.635A pdb=" N ALA B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 933 " --> pdb=" O PHE B 929 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 934 " --> pdb=" O ASN B 930 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP B 938 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 941 " --> pdb=" O GLN B 937 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.727A pdb=" N LEU B 961 " --> pdb=" O ASN B 957 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 966 " --> pdb=" O ASN B 962 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 967 " --> pdb=" O THR B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 980 No H-bonds generated for 'chain 'B' and resid 978 through 980' Processing helix chain 'B' and resid 981 through 986 removed outlier: 4.388A pdb=" N ARG B 985 " --> pdb=" O ASP B 981 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 986 " --> pdb=" O ILE B 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 981 through 986' Processing helix chain 'B' and resid 987 through 1034 removed outlier: 3.521A pdb=" N GLY B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1120 No H-bonds generated for 'chain 'B' and resid 1118 through 1120' Processing helix chain 'B' and resid 1143 through 1148 removed outlier: 3.848A pdb=" N ASP B1148 " --> pdb=" O GLN B1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1156 Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.635A pdb=" N LYS C 388 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 635 through 640 removed outlier: 3.801A pdb=" N TYR C 638 " --> pdb=" O TRP C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 removed outlier: 3.572A pdb=" N TYR C 743 " --> pdb=" O ASP C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.852A pdb=" N ASN C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 759 removed outlier: 3.605A pdb=" N GLY C 759 " --> pdb=" O LEU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 785 removed outlier: 3.725A pdb=" N ASP C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 785 " --> pdb=" O GLN C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 828 removed outlier: 3.970A pdb=" N ASN C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS C 827 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 858 removed outlier: 4.147A pdb=" N LYS C 856 " --> pdb=" O CYS C 853 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 857 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 886 removed outlier: 3.733A pdb=" N ILE C 884 " --> pdb=" O LEU C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 892 removed outlier: 3.526A pdb=" N GLY C 891 " --> pdb=" O TRP C 888 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 892 " --> pdb=" O THR C 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 888 through 892' Processing helix chain 'C' and resid 899 through 908 removed outlier: 3.588A pdb=" N TYR C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 908 " --> pdb=" O MET C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 920 removed outlier: 3.864A pdb=" N LEU C 918 " --> pdb=" O GLN C 915 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR C 919 " --> pdb=" O ASN C 916 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU C 920 " --> pdb=" O VAL C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 935 removed outlier: 4.252A pdb=" N ASN C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 943 removed outlier: 3.632A pdb=" N SER C 942 " --> pdb=" O ASP C 938 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 957 removed outlier: 4.265A pdb=" N VAL C 953 " --> pdb=" O LYS C 949 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN C 957 " --> pdb=" O VAL C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 968 through 970 No H-bonds generated for 'chain 'C' and resid 968 through 970' Processing helix chain 'C' and resid 981 through 985 Processing helix chain 'C' and resid 987 through 1034 removed outlier: 4.593A pdb=" N GLU C 992 " --> pdb=" O PRO C 988 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 993 " --> pdb=" O PRO C 989 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C1000 " --> pdb=" O ASP C 996 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG C1002 " --> pdb=" O LEU C 998 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C1015 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1162 Processing helix chain 'I' and resid 65 through 69 removed outlier: 3.919A pdb=" N LEU I 69 " --> pdb=" O LYS I 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.883A pdb=" N THR G 92 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.496A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ASN A 61 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR A 271 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 63 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 269 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 266 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.860A pdb=" N ASP A 289 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.091A pdb=" N ARG A 236 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE A 106 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN A 238 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TRP A 104 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A 240 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 314 removed outlier: 4.304A pdb=" N THR A 601 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 removed outlier: 4.304A pdb=" N THR A 601 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 596 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 330 removed outlier: 6.539A pdb=" N GLU A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ASN A 544 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 328 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 541 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 543 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 550 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 545 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 364 removed outlier: 6.685A pdb=" N CYS A 363 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 526 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'A' and resid 454 through 456 Processing sheet with id=AB1, first strand: chain 'A' and resid 656 through 657 removed outlier: 6.407A pdb=" N GLU A 656 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 674 " --> pdb=" O PRO A 667 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 714 through 721 removed outlier: 6.608A pdb=" N ALA A 715 " --> pdb=" O ASN A1076 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN A1076 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU A1074 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A1061 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A1058 " --> pdb=" O GLY A1061 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A1052 " --> pdb=" O VAL A1067 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR A1069 " --> pdb=" O HIS A1050 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1050 " --> pdb=" O TYR A1069 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 724 through 730 removed outlier: 3.572A pdb=" N ALA A1080 " --> pdb=" O PHE A1097 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A1097 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A1096 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A1107 " --> pdb=" O VAL A1096 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1122 through 1127 removed outlier: 4.776A pdb=" N ALA A1089 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A1084 " --> pdb=" O VAL A1135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.207A pdb=" N ALA B 266 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 200 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 226 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.558A pdb=" N HIS B 49 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.558A pdb=" N HIS B 49 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 289 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 84 removed outlier: 4.185A pdb=" N PHE B 237 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B 238 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TRP B 104 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 240 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 115 through 120 Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.522A pdb=" N GLY B 313 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 601 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.672A pdb=" N ILE B 328 " --> pdb=" O ASN B 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AC5, first strand: chain 'B' and resid 402 through 403 removed outlier: 3.868A pdb=" N VAL B 512 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 456 removed outlier: 3.600A pdb=" N TYR B 455 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 495 " --> pdb=" O TYR B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 475 through 476 removed outlier: 3.606A pdb=" N TYR B 475 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 491 " --> pdb=" O TYR B 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 553 through 556 removed outlier: 3.960A pdb=" N THR B 590 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 661 through 662 removed outlier: 4.007A pdb=" N TYR B 662 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 693 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 677 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 695 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 675 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 668 " --> pdb=" O ILE B 672 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 717 Processing sheet with id=AD2, first strand: chain 'B' and resid 720 through 721 removed outlier: 3.572A pdb=" N VAL B1070 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 720 through 721 removed outlier: 3.572A pdb=" N VAL B1070 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B1067 " --> pdb=" O LEU B1051 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 728 through 729 removed outlier: 3.689A pdb=" N GLY B1061 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B1058 " --> pdb=" O GLY B1061 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.546A pdb=" N THR B 861 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1122 through 1124 removed outlier: 3.536A pdb=" N CYS B1084 " --> pdb=" O VAL B1135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1096 through 1099 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.784A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN C 61 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C 271 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 63 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 269 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR C 267 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA C 266 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.851A pdb=" N ASP C 289 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.903A pdb=" N PHE C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 313 through 314 removed outlier: 4.018A pdb=" N THR C 601 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 598 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 326 through 327 removed outlier: 7.608A pdb=" N GLU C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 550 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 357 through 360 removed outlier: 3.994A pdb=" N ILE C 360 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 397 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 455 through 456 removed outlier: 3.975A pdb=" N ARG C 495 " --> pdb=" O TYR C 455 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 656 through 662 removed outlier: 3.755A pdb=" N ALA C 696 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR C 698 " --> pdb=" O VAL C 658 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN C 660 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 697 " --> pdb=" O CYS C 673 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS C 673 " --> pdb=" O TYR C 697 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 666 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 713 through 717 removed outlier: 4.094A pdb=" N ALA C1080 " --> pdb=" O PHE C1097 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C1097 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 720 through 721 removed outlier: 3.789A pdb=" N MET C1052 " --> pdb=" O VAL C1067 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR C1069 " --> pdb=" O HIS C1050 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS C1050 " --> pdb=" O TYR C1069 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 724 through 730 Processing sheet with id=AF1, first strand: chain 'C' and resid 736 through 738 Processing sheet with id=AF2, first strand: chain 'C' and resid 1122 through 1124 removed outlier: 3.552A pdb=" N CYS C1084 " --> pdb=" O VAL C1135 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.550A pdb=" N THR H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.144A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 11 through 12 removed outlier: 8.020A pdb=" N VAL I 12 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA I 116 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR I 94 " --> pdb=" O GLN I 41 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.595A pdb=" N LYS K 107 " --> pdb=" O VAL K 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.678A pdb=" N ILE K 18 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 47 through 50 removed outlier: 5.206A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER K 92 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA K 101 " --> pdb=" O SER K 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.922A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AG4, first strand: chain 'L' and resid 44 through 50 removed outlier: 7.336A pdb=" N HIS L 41 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.860A pdb=" N THR G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.846A pdb=" N VAL G 36 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU G 52 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP G 38 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG8, first strand: chain 'J' and resid 47 through 51 removed outlier: 5.551A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) 863 hydrogen bonds defined for protein. 2322 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: 16.27 Time building geometry restraints manager: 13.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9609 1.34 - 1.46: 8121 1.46 - 1.59: 14379 1.59 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 32289 Sorted by residual: bond pdb=" C PRO B 988 " pdb=" N PRO B 989 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" N ASN B 333 " pdb=" CA ASN B 333 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.78e+00 bond pdb=" N ILE B 334 " pdb=" CA ILE B 334 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.19e-02 7.06e+03 7.19e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" N THR B 335 " pdb=" CA THR B 335 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.16e-02 7.43e+03 5.44e+00 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.85: 793 105.85 - 113.85: 17961 113.85 - 121.85: 17698 121.85 - 129.86: 7352 129.86 - 137.86: 155 Bond angle restraints: 43959 Sorted by residual: angle pdb=" C MET G 87 " pdb=" N ASP G 88 " pdb=" CA ASP G 88 " ideal model delta sigma weight residual 122.65 135.57 -12.92 1.66e+00 3.63e-01 6.06e+01 angle pdb=" C ASN B 333 " pdb=" CA ASN B 333 " pdb=" CB ASN B 333 " ideal model delta sigma weight residual 109.72 99.36 10.36 1.66e+00 3.63e-01 3.90e+01 angle pdb=" N PRO B 332 " pdb=" CA PRO B 332 " pdb=" C PRO B 332 " ideal model delta sigma weight residual 111.41 119.25 -7.84 1.50e+00 4.44e-01 2.73e+01 angle pdb=" C HIS B 143 " pdb=" N LYS B 144 " pdb=" CA LYS B 144 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C ALA A 572 " pdb=" N ASP A 573 " pdb=" CA ASP A 573 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 ... (remaining 43954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17619 17.77 - 35.54: 1704 35.54 - 53.31: 285 53.31 - 71.07: 70 71.07 - 88.84: 29 Dihedral angle restraints: 19707 sinusoidal: 8133 harmonic: 11574 Sorted by residual: dihedral pdb=" CB CYS B 482 " pdb=" SG CYS B 482 " pdb=" SG CYS B 490 " pdb=" CB CYS B 490 " ideal model delta sinusoidal sigma weight residual 93.00 175.28 -82.28 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CA LYS B 446 " pdb=" C LYS B 446 " pdb=" N VAL B 447 " pdb=" CA VAL B 447 " ideal model delta harmonic sigma weight residual 180.00 -135.04 -44.96 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CB CYS A 664 " pdb=" SG CYS A 664 " pdb=" SG CYS A 673 " pdb=" CB CYS A 673 " ideal model delta sinusoidal sigma weight residual 93.00 173.51 -80.51 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 19704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4213 0.074 - 0.148: 765 0.148 - 0.222: 83 0.222 - 0.297: 8 0.297 - 0.371: 4 Chirality restraints: 5073 Sorted by residual: chirality pdb=" C2 NAG A1312 " pdb=" C1 NAG A1312 " pdb=" C3 NAG A1312 " pdb=" N2 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL A 622 " pdb=" CA VAL A 622 " pdb=" CG1 VAL A 622 " pdb=" CG2 VAL A 622 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 284 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 5070 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " 0.326 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG B1303 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " -0.295 2.00e-02 2.50e+03 2.60e-01 8.42e+02 pdb=" C7 NAG B1305 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " -0.049 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 37 " 0.032 2.00e-02 2.50e+03 2.84e-02 2.02e+01 pdb=" CG TRP K 37 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP K 37 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP K 37 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 37 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 37 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP K 37 " 0.004 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6180 2.78 - 3.31: 27321 3.31 - 3.84: 51610 3.84 - 4.37: 56191 4.37 - 4.90: 97275 Nonbonded interactions: 238577 Sorted by model distance: nonbonded pdb=" OG SER C 152 " pdb=" OE1 GLU C 153 " model vdw 2.248 2.440 nonbonded pdb=" O ALA C 881 " pdb=" OG1 THR C 885 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR C 647 " pdb=" O GLY C 650 " model vdw 2.272 2.440 nonbonded pdb=" O ASN B 441 " pdb=" OG SER B 445 " model vdw 2.274 2.440 nonbonded pdb=" O GLN C1007 " pdb=" OG1 THR C1011 " model vdw 2.291 2.440 ... (remaining 238572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.700 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 86.870 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32289 Z= 0.272 Angle : 0.914 13.070 43959 Z= 0.468 Chirality : 0.057 0.371 5073 Planarity : 0.009 0.283 5616 Dihedral : 14.054 88.843 12138 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.32 % Rotamer: Outliers : 0.12 % Allowed : 0.69 % Favored : 99.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.60 (0.12), residues: 3939 helix: -2.46 (0.16), residues: 595 sheet: -0.49 (0.18), residues: 874 loop : -2.10 (0.11), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP K 37 HIS 0.015 0.001 HIS B 956 PHE 0.029 0.002 PHE C 344 TYR 0.026 0.002 TYR I 95 ARG 0.018 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7260 (t80) cc_final: 0.6439 (t80) REVERT: A 464 LYS cc_start: 0.8450 (mptt) cc_final: 0.8207 (mmtm) REVERT: C 629 ASP cc_start: 0.6985 (t0) cc_final: 0.6727 (t0) REVERT: H 88 ASP cc_start: 0.8901 (t0) cc_final: 0.8613 (t0) REVERT: I 87 MET cc_start: 0.3967 (ppp) cc_final: 0.2104 (tpt) REVERT: K 32 PHE cc_start: 0.8148 (m-80) cc_final: 0.7945 (m-80) REVERT: K 89 TYR cc_start: 0.7359 (m-10) cc_final: 0.7140 (m-80) REVERT: K 108 LEU cc_start: 0.6249 (mp) cc_final: 0.5831 (mt) REVERT: G 5 LYS cc_start: 0.8376 (pptt) cc_final: 0.7965 (tppt) REVERT: G 54 TYR cc_start: 0.7254 (m-80) cc_final: 0.6787 (m-80) REVERT: G 73 MET cc_start: 0.6647 (tpp) cc_final: 0.6131 (tpp) REVERT: G 87 MET cc_start: 0.2724 (mpp) cc_final: 0.0309 (ptm) REVERT: G 101 LYS cc_start: 0.8504 (tptt) cc_final: 0.8175 (ttmm) outliers start: 4 outliers final: 2 residues processed: 229 average time/residue: 0.4281 time to fit residues: 162.8148 Evaluate side-chains 154 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 583 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 7.9990 chunk 297 optimal weight: 0.0370 chunk 165 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 187 optimal weight: 0.0770 chunk 229 optimal weight: 9.9990 chunk 356 optimal weight: 40.0000 overall best weight: 3.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 238 GLN A 937 GLN A1007 GLN ** A1050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN C 146 ASN C 185 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 ASN C 921 ASN ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN L 39 GLN G 100 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32289 Z= 0.344 Angle : 0.678 10.258 43959 Z= 0.348 Chirality : 0.046 0.256 5073 Planarity : 0.005 0.061 5616 Dihedral : 6.751 59.173 5027 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.54 % Rotamer: Outliers : 0.93 % Allowed : 9.66 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.37 (0.12), residues: 3939 helix: -1.34 (0.19), residues: 658 sheet: -0.67 (0.18), residues: 849 loop : -2.07 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 37 HIS 0.009 0.002 HIS A 627 PHE 0.034 0.002 PHE B 825 TYR 0.021 0.002 TYR B 167 ARG 0.009 0.001 ARG I 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 3.768 Fit side-chains revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7315 (t80) cc_final: 0.6335 (t80) REVERT: A 464 LYS cc_start: 0.8394 (mptt) cc_final: 0.8131 (mmtm) REVERT: A 699 MET cc_start: 0.8563 (mpp) cc_final: 0.8348 (mpp) REVERT: B 167 TYR cc_start: 0.7575 (t80) cc_final: 0.7232 (t80) REVERT: C 128 ILE cc_start: 0.2821 (OUTLIER) cc_final: 0.2612 (pt) REVERT: C 629 ASP cc_start: 0.7280 (t0) cc_final: 0.7023 (t0) REVERT: C 699 MET cc_start: 0.8566 (mpp) cc_final: 0.8070 (mpp) REVERT: I 84 MET cc_start: 0.2625 (OUTLIER) cc_final: 0.1431 (ttt) REVERT: I 87 MET cc_start: 0.4856 (ppp) cc_final: 0.3718 (ppp) REVERT: K 32 PHE cc_start: 0.8178 (m-80) cc_final: 0.7891 (m-80) REVERT: G 5 LYS cc_start: 0.8295 (pptt) cc_final: 0.7919 (pptt) REVERT: G 73 MET cc_start: 0.6557 (tpp) cc_final: 0.6001 (tpt) REVERT: G 84 MET cc_start: 0.2332 (mpp) cc_final: 0.1758 (mpp) REVERT: G 109 TRP cc_start: 0.4846 (m100) cc_final: 0.4562 (m100) REVERT: J 41 HIS cc_start: 0.7530 (t70) cc_final: 0.7228 (t70) outliers start: 32 outliers final: 18 residues processed: 189 average time/residue: 0.4164 time to fit residues: 133.5294 Evaluate side-chains 166 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 491 TYR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 976 SER Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 104 TYR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 0.0270 chunk 297 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 357 optimal weight: 30.0000 chunk 386 optimal weight: 20.0000 chunk 318 optimal weight: 3.9990 chunk 354 optimal weight: 20.0000 chunk 121 optimal weight: 0.0770 chunk 286 optimal weight: 4.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 ASN C 903 GLN ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 32289 Z= 0.153 Angle : 0.565 10.448 43959 Z= 0.285 Chirality : 0.044 0.254 5073 Planarity : 0.005 0.069 5616 Dihedral : 6.136 57.457 5026 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.01 % Rotamer: Outliers : 0.95 % Allowed : 12.89 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.02 (0.13), residues: 3939 helix: -0.62 (0.20), residues: 651 sheet: -0.55 (0.18), residues: 849 loop : -1.93 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP K 37 HIS 0.007 0.001 HIS B 143 PHE 0.025 0.001 PHE B 825 TYR 0.013 0.001 TYR B 353 ARG 0.002 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7232 (t80) cc_final: 0.6345 (t80) REVERT: A 140 PHE cc_start: 0.6509 (p90) cc_final: 0.6222 (p90) REVERT: A 222 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7631 (tt) REVERT: A 464 LYS cc_start: 0.8390 (mptt) cc_final: 0.8132 (mmtm) REVERT: A 629 ASP cc_start: 0.7536 (t0) cc_final: 0.7282 (t70) REVERT: B 167 TYR cc_start: 0.7515 (t80) cc_final: 0.7180 (t80) REVERT: B 174 MET cc_start: -0.2697 (mmt) cc_final: -0.3551 (mtt) REVERT: C 128 ILE cc_start: 0.3357 (OUTLIER) cc_final: 0.2900 (pt) REVERT: C 629 ASP cc_start: 0.7203 (t0) cc_final: 0.6907 (t0) REVERT: I 84 MET cc_start: 0.2539 (mmp) cc_final: 0.1238 (ttt) REVERT: I 87 MET cc_start: 0.4721 (ppp) cc_final: 0.3512 (ppp) REVERT: K 32 PHE cc_start: 0.8279 (m-80) cc_final: 0.7982 (m-80) REVERT: G 73 MET cc_start: 0.6665 (tpp) cc_final: 0.6117 (tpt) REVERT: G 109 TRP cc_start: 0.4849 (m100) cc_final: 0.4632 (m100) REVERT: J 41 HIS cc_start: 0.7401 (t70) cc_final: 0.7071 (t70) REVERT: J 51 TYR cc_start: 0.7339 (p90) cc_final: 0.7095 (p90) outliers start: 33 outliers final: 20 residues processed: 184 average time/residue: 0.4101 time to fit residues: 128.4837 Evaluate side-chains 172 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 491 TYR Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 TYR Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 30.0000 chunk 268 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 170 optimal weight: 0.4980 chunk 240 optimal weight: 40.0000 chunk 358 optimal weight: 30.0000 chunk 379 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 544 ASN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 779 ASN C 903 GLN C 915 GLN C1025 ASN ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32289 Z= 0.374 Angle : 0.665 10.007 43959 Z= 0.342 Chirality : 0.046 0.232 5073 Planarity : 0.005 0.073 5616 Dihedral : 6.416 59.898 5026 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.27 % Rotamer: Outliers : 1.99 % Allowed : 15.15 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.13), residues: 3939 helix: -0.77 (0.20), residues: 661 sheet: -0.79 (0.18), residues: 853 loop : -1.99 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP K 37 HIS 0.011 0.002 HIS G 100 PHE 0.026 0.002 PHE C 594 TYR 0.022 0.002 TYR C 638 ARG 0.007 0.001 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 162 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7353 (t80) cc_final: 0.6398 (t80) REVERT: A 140 PHE cc_start: 0.6467 (p90) cc_final: 0.6089 (p90) REVERT: B 167 TYR cc_start: 0.7554 (t80) cc_final: 0.7264 (t80) REVERT: B 174 MET cc_start: -0.1941 (mmt) cc_final: -0.2936 (mtt) REVERT: B 902 MET cc_start: 0.8224 (mtm) cc_final: 0.7760 (mtm) REVERT: C 629 ASP cc_start: 0.7371 (t0) cc_final: 0.7106 (t0) REVERT: C 699 MET cc_start: 0.8593 (mpp) cc_final: 0.8307 (mpp) REVERT: I 84 MET cc_start: 0.2785 (mmp) cc_final: 0.1363 (ttt) REVERT: I 87 MET cc_start: 0.4862 (ppp) cc_final: 0.3832 (ppp) REVERT: K 32 PHE cc_start: 0.8236 (m-80) cc_final: 0.7937 (m-80) REVERT: G 73 MET cc_start: 0.6405 (tpp) cc_final: 0.6048 (tpp) REVERT: G 109 TRP cc_start: 0.5071 (m100) cc_final: 0.4766 (m100) REVERT: J 41 HIS cc_start: 0.7703 (t70) cc_final: 0.7379 (t70) REVERT: J 51 TYR cc_start: 0.7406 (p90) cc_final: 0.7179 (p90) outliers start: 69 outliers final: 42 residues processed: 220 average time/residue: 0.3824 time to fit residues: 145.5071 Evaluate side-chains 192 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1135 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 976 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 TYR Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 3.9990 chunk 215 optimal weight: 0.0370 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 0.6980 chunk 156 optimal weight: 40.0000 chunk 324 optimal weight: 5.9990 chunk 262 optimal weight: 0.0770 chunk 0 optimal weight: 40.0000 chunk 193 optimal weight: 0.9990 chunk 340 optimal weight: 30.0000 chunk 95 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1004 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 ASN C 903 GLN C 915 GLN ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32289 Z= 0.142 Angle : 0.560 11.162 43959 Z= 0.282 Chirality : 0.044 0.239 5073 Planarity : 0.004 0.075 5616 Dihedral : 5.766 57.770 5025 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.24 % Allowed : 16.71 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3939 helix: -0.17 (0.21), residues: 648 sheet: -0.67 (0.18), residues: 869 loop : -1.83 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP K 37 HIS 0.007 0.001 HIS A 627 PHE 0.020 0.001 PHE B 92 TYR 0.030 0.001 TYR K 38 ARG 0.007 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7240 (t80) cc_final: 0.6307 (t80) REVERT: A 140 PHE cc_start: 0.6449 (p90) cc_final: 0.6043 (p90) REVERT: B 150 MET cc_start: 0.5015 (tpp) cc_final: 0.4202 (tpt) REVERT: B 167 TYR cc_start: 0.7549 (t80) cc_final: 0.7285 (t80) REVERT: B 174 MET cc_start: -0.2381 (mmt) cc_final: -0.3100 (mtt) REVERT: B 902 MET cc_start: 0.7832 (mtm) cc_final: 0.7527 (mtm) REVERT: C 629 ASP cc_start: 0.7248 (t0) cc_final: 0.6950 (t0) REVERT: I 84 MET cc_start: 0.2454 (OUTLIER) cc_final: 0.1614 (mmp) REVERT: K 32 PHE cc_start: 0.8234 (m-80) cc_final: 0.7944 (m-80) REVERT: K 89 TYR cc_start: 0.6629 (m-80) cc_final: 0.5816 (t80) REVERT: G 5 LYS cc_start: 0.8271 (pptt) cc_final: 0.7549 (tppt) REVERT: G 54 TYR cc_start: 0.7058 (m-80) cc_final: 0.6721 (m-80) REVERT: G 73 MET cc_start: 0.6498 (tpp) cc_final: 0.6100 (tpp) REVERT: G 84 MET cc_start: 0.1877 (mpp) cc_final: 0.1545 (mpp) REVERT: J 37 TRP cc_start: 0.5568 (m100) cc_final: 0.5360 (m100) REVERT: J 41 HIS cc_start: 0.7656 (t70) cc_final: 0.7311 (t70) REVERT: J 51 TYR cc_start: 0.7351 (p90) cc_final: 0.7123 (p90) outliers start: 43 outliers final: 28 residues processed: 199 average time/residue: 0.4200 time to fit residues: 142.5967 Evaluate side-chains 182 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 104 TYR Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 380 optimal weight: 8.9990 chunk 315 optimal weight: 0.3980 chunk 176 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN ** C1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32289 Z= 0.169 Angle : 0.565 9.821 43959 Z= 0.283 Chirality : 0.044 0.236 5073 Planarity : 0.004 0.075 5616 Dihedral : 5.557 58.281 5025 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.62 % Allowed : 17.32 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.76 (0.13), residues: 3939 helix: -0.02 (0.21), residues: 651 sheet: -0.61 (0.18), residues: 869 loop : -1.79 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP K 37 HIS 0.006 0.001 HIS G 100 PHE 0.020 0.001 PHE B 92 TYR 0.021 0.001 TYR I 108 ARG 0.003 0.000 ARG A1109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 161 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7274 (t80) cc_final: 0.6321 (t80) REVERT: A 140 PHE cc_start: 0.6530 (p90) cc_final: 0.6129 (p90) REVERT: A 276 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 167 TYR cc_start: 0.7575 (t80) cc_final: 0.7313 (t80) REVERT: B 174 MET cc_start: -0.2318 (mmt) cc_final: -0.2998 (mtt) REVERT: B 902 MET cc_start: 0.7958 (mtm) cc_final: 0.7669 (mtm) REVERT: C 627 HIS cc_start: 0.7024 (m90) cc_final: 0.6752 (m90) REVERT: C 629 ASP cc_start: 0.7300 (t0) cc_final: 0.6990 (t0) REVERT: C 699 MET cc_start: 0.8452 (mpp) cc_final: 0.8204 (mpp) REVERT: I 84 MET cc_start: 0.2596 (OUTLIER) cc_final: 0.1743 (mmp) REVERT: K 32 PHE cc_start: 0.8190 (m-80) cc_final: 0.7867 (m-80) REVERT: K 89 TYR cc_start: 0.6566 (m-80) cc_final: 0.5864 (t80) REVERT: G 5 LYS cc_start: 0.8309 (pptt) cc_final: 0.7602 (tppt) REVERT: G 54 TYR cc_start: 0.7113 (m-80) cc_final: 0.6814 (m-80) REVERT: G 73 MET cc_start: 0.6434 (tpp) cc_final: 0.6074 (tpp) REVERT: G 84 MET cc_start: 0.1827 (mpp) cc_final: 0.1554 (mpp) REVERT: J 41 HIS cc_start: 0.7661 (t70) cc_final: 0.7309 (t70) REVERT: J 51 TYR cc_start: 0.7345 (p90) cc_final: 0.7099 (p90) REVERT: J 88 TYR cc_start: 0.1294 (m-80) cc_final: 0.0975 (m-80) outliers start: 56 outliers final: 37 residues processed: 204 average time/residue: 0.4004 time to fit residues: 141.8289 Evaluate side-chains 195 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 104 TYR Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 100 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 216 optimal weight: 0.0020 chunk 277 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 320 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 378 optimal weight: 0.6980 chunk 237 optimal weight: 0.0870 chunk 230 optimal weight: 50.0000 chunk 174 optimal weight: 3.9990 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 GLN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32289 Z= 0.136 Angle : 0.553 9.483 43959 Z= 0.276 Chirality : 0.043 0.241 5073 Planarity : 0.004 0.075 5616 Dihedral : 5.291 57.828 5025 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.50 % Allowed : 17.87 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.62 (0.13), residues: 3939 helix: 0.18 (0.21), residues: 650 sheet: -0.52 (0.18), residues: 863 loop : -1.72 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP K 37 HIS 0.013 0.001 HIS G 100 PHE 0.029 0.001 PHE B 492 TYR 0.033 0.001 TYR B 353 ARG 0.002 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 167 time to evaluate : 3.727 Fit side-chains revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7306 (t80) cc_final: 0.6307 (t80) REVERT: A 140 PHE cc_start: 0.6503 (p90) cc_final: 0.6116 (p90) REVERT: A 276 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 464 LYS cc_start: 0.8383 (mptt) cc_final: 0.8157 (mmtm) REVERT: A 673 CYS cc_start: 0.6414 (OUTLIER) cc_final: 0.6110 (p) REVERT: B 144 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6619 (tmtt) REVERT: B 174 MET cc_start: -0.2326 (mmt) cc_final: -0.2969 (mtt) REVERT: C 627 HIS cc_start: 0.6877 (m90) cc_final: 0.6614 (m90) REVERT: C 629 ASP cc_start: 0.7226 (t0) cc_final: 0.6914 (t0) REVERT: C 902 MET cc_start: 0.7638 (tpp) cc_final: 0.7408 (ttm) REVERT: I 84 MET cc_start: 0.2569 (OUTLIER) cc_final: 0.1411 (mmp) REVERT: I 87 MET cc_start: 0.4293 (ppp) cc_final: 0.1363 (tpt) REVERT: K 32 PHE cc_start: 0.8178 (m-80) cc_final: 0.7853 (m-80) REVERT: G 73 MET cc_start: 0.6471 (tpp) cc_final: 0.6116 (tpp) REVERT: J 41 HIS cc_start: 0.7648 (t70) cc_final: 0.7292 (t70) REVERT: J 51 TYR cc_start: 0.7334 (p90) cc_final: 0.7130 (p90) outliers start: 52 outliers final: 34 residues processed: 208 average time/residue: 0.3818 time to fit residues: 135.4711 Evaluate side-chains 190 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 104 TYR Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 226 optimal weight: 0.6980 chunk 114 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: