Starting phenix.real_space_refine on Thu Mar 21 09:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyz_26200/03_2024/7tyz_26200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyz_26200/03_2024/7tyz_26200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyz_26200/03_2024/7tyz_26200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyz_26200/03_2024/7tyz_26200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyz_26200/03_2024/7tyz_26200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyz_26200/03_2024/7tyz_26200.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 129 5.16 5 C 18870 2.51 5 N 4899 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 127": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29736 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "C" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 7 Chain: "D" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "E" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 6 Chain: "F" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.93, per 1000 atoms: 0.54 Number of scatterers: 29736 At special positions: 0 Unit cell: (162.378, 159.759, 222.615, 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 129 16.00 O 5838 8.00 N 4899 7.00 C 18870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 603 " " NAG E1303 " - " ASN E 616 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 234 " " NAG E1306 " - " ASN E 165 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A 282 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN E 331 " " NAG T 1 " - " ASN E 709 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 282 " " NAG X 1 " - " ASN E 343 " Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 5.5 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 51 sheets defined 28.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.588A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.774A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.857A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.622A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.702A pdb=" N ALA A 623 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.265A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.821A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.659A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.517A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.547A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.180A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 27 through 37 removed outlier: 3.574A pdb=" N GLY B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.253A pdb=" N VAL B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.599A pdb=" N ASN B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.857A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.514A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.892A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.677A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.755A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.519A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.796A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.521A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.589A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.576A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.590A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.208A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 36 removed outlier: 3.533A pdb=" N ASN D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.094A pdb=" N VAL D 96 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.631A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 301 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.842A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.644A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.255A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN E 764 " --> pdb=" O CYS E 760 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 783 " --> pdb=" O GLN E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.797A pdb=" N GLN E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 883 " --> pdb=" O ALA E 879 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 907 Processing helix chain 'E' and resid 913 through 919 removed outlier: 3.608A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.542A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.675A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 983 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.247A pdb=" N GLU E 990 " --> pdb=" O PRO E 986 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1146 Processing helix chain 'F' and resid 16 through 25 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.579A pdb=" N GLU F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 123 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 158 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.025A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.853A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.625A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.801A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 145 removed outlier: 6.259A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 318 removed outlier: 5.464A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.827A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 659 removed outlier: 6.247A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.564A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.960A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 removed outlier: 6.463A pdb=" N ALA E 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.681A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.197A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.538A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.580A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.437A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.503A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.503A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 659 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.528A pdb=" N ALA C 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.963A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.943A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.917A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 263 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 50 through 55 removed outlier: 3.859A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 141 through 145 removed outlier: 6.502A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 310 through 318 removed outlier: 5.440A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 650 " --> pdb=" O PHE E 643 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 310 through 318 removed outlier: 5.440A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.996A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.996A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 510 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 452 through 453 removed outlier: 3.789A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 659 removed outlier: 6.222A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 712 through 715 Processing sheet with id=AF3, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.956A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 735 through 736 Processing sheet with id=AF5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 5.054A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1094 through 1097 1027 hydrogen bonds defined for protein. 2799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.74 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9527 1.34 - 1.47: 7444 1.47 - 1.59: 13243 1.59 - 1.71: 2 1.71 - 1.83: 165 Bond restraints: 30381 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.614 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C1 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 30376 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.17: 553 105.17 - 112.38: 15696 112.38 - 119.58: 9621 119.58 - 126.78: 15123 126.78 - 133.98: 347 Bond angle restraints: 41340 Sorted by residual: angle pdb=" CA LYS C 462 " pdb=" CB LYS C 462 " pdb=" CG LYS C 462 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C GLY C 404 " pdb=" N ASP C 405 " pdb=" CA ASP C 405 " ideal model delta sigma weight residual 120.38 125.06 -4.68 1.46e+00 4.69e-01 1.03e+01 angle pdb=" N GLN F 166 " pdb=" CA GLN F 166 " pdb=" CB GLN F 166 " ideal model delta sigma weight residual 110.39 115.23 -4.84 1.66e+00 3.63e-01 8.51e+00 angle pdb=" C SER E 359 " pdb=" N ASN E 360 " pdb=" CA ASN E 360 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" C CYS A 131 " pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sigma weight residual 114.41 108.05 6.36 2.30e+00 1.89e-01 7.66e+00 ... (remaining 41335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 17694 24.34 - 48.68: 970 48.68 - 73.02: 161 73.02 - 97.36: 76 97.36 - 121.71: 65 Dihedral angle restraints: 18966 sinusoidal: 8211 harmonic: 10755 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 11.73 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 14.56 78.44 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 15.19 77.81 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 18963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4857 0.159 - 0.319: 27 0.319 - 0.478: 6 0.478 - 0.637: 1 0.637 - 0.797: 2 Chirality restraints: 4893 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN E 282 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4890 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 282 " 0.036 2.00e-02 2.50e+03 3.26e-02 1.33e+01 pdb=" CG ASN E 282 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 282 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN E 282 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO C1143 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.027 2.00e-02 2.50e+03 2.62e-02 8.60e+00 pdb=" CG ASN A 616 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.020 2.00e-02 2.50e+03 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 715 2.68 - 3.24: 28527 3.24 - 3.79: 43990 3.79 - 4.35: 56725 4.35 - 4.90: 93907 Nonbonded interactions: 223864 Sorted by model distance: nonbonded pdb=" OG1 THR E 676 " pdb=" O SER E 691 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR C 676 " pdb=" O SER C 691 " model vdw 2.139 2.440 nonbonded pdb=" OD1 ASN A 616 " pdb=" N2 NAG A1303 " model vdw 2.169 2.520 nonbonded pdb=" OG SER A 803 " pdb=" OE1 GLN A 804 " model vdw 2.196 2.440 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.199 2.440 ... (remaining 223859 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.010 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: 0.040 Extract box with map and model: 29.180 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 79.330 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.410 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 0.091 30381 Z= 0.255 Angle : 0.635 9.029 41340 Z= 0.304 Chirality : 0.052 0.797 4893 Planarity : 0.004 0.078 5277 Dihedral : 17.212 121.706 11922 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3663 helix: 1.14 (0.18), residues: 948 sheet: -0.60 (0.19), residues: 738 loop : -2.22 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.005 0.001 HIS B 52 PHE 0.016 0.001 PHE E 157 TYR 0.020 0.001 TYR A 421 ARG 0.004 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 147 LYS cc_start: 0.5170 (mmtm) cc_final: 0.4925 (mttm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3956 time to fit residues: 123.7658 Evaluate side-chains 127 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.7980 chunk 279 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 335 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 370 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1106 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 30381 Z= 0.419 Angle : 0.716 9.915 41340 Z= 0.352 Chirality : 0.049 0.378 4893 Planarity : 0.005 0.068 5277 Dihedral : 12.358 100.625 5322 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.87 % Allowed : 8.50 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3663 helix: 0.79 (0.17), residues: 942 sheet: -0.85 (0.18), residues: 735 loop : -2.34 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 152 HIS 0.006 0.001 HIS E 146 PHE 0.030 0.002 PHE C 906 TYR 0.025 0.002 TYR A 421 ARG 0.005 0.001 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 LYS cc_start: 0.5441 (mmtm) cc_final: 0.4745 (mttm) outliers start: 28 outliers final: 18 residues processed: 161 average time/residue: 0.3698 time to fit residues: 101.2272 Evaluate side-chains 137 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 335 optimal weight: 0.8980 chunk 362 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 332 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30381 Z= 0.167 Angle : 0.588 10.850 41340 Z= 0.284 Chirality : 0.045 0.337 4893 Planarity : 0.004 0.067 5277 Dihedral : 10.760 100.981 5322 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.09 % Allowed : 11.18 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3663 helix: 1.05 (0.18), residues: 942 sheet: -0.69 (0.19), residues: 738 loop : -2.27 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 152 HIS 0.006 0.001 HIS A 146 PHE 0.015 0.001 PHE A 823 TYR 0.024 0.001 TYR A 351 ARG 0.004 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 3.263 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8572 (t80) REVERT: A 583 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 147 LYS cc_start: 0.5360 (mmtm) cc_final: 0.4517 (mttm) outliers start: 35 outliers final: 21 residues processed: 168 average time/residue: 0.3678 time to fit residues: 104.7536 Evaluate side-chains 145 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E1106 GLN F 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30381 Z= 0.227 Angle : 0.595 11.653 41340 Z= 0.288 Chirality : 0.045 0.336 4893 Planarity : 0.004 0.068 5277 Dihedral : 9.567 97.617 5322 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 1.62 % Allowed : 12.53 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3663 helix: 1.12 (0.18), residues: 939 sheet: -0.69 (0.19), residues: 744 loop : -2.20 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 353 HIS 0.007 0.001 HIS E 146 PHE 0.015 0.001 PHE C 157 TYR 0.026 0.001 TYR A 351 ARG 0.005 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 130 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8553 (t80) REVERT: C 583 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 147 LYS cc_start: 0.5370 (mmtm) cc_final: 0.4566 (mttm) outliers start: 52 outliers final: 32 residues processed: 170 average time/residue: 0.3720 time to fit residues: 108.8181 Evaluate side-chains 156 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 265 optimal weight: 0.0270 chunk 147 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30381 Z= 0.311 Angle : 0.630 10.167 41340 Z= 0.308 Chirality : 0.046 0.325 4893 Planarity : 0.004 0.076 5277 Dihedral : 8.962 93.368 5322 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 1.81 % Allowed : 14.18 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3663 helix: 0.97 (0.17), residues: 942 sheet: -0.85 (0.18), residues: 765 loop : -2.26 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 152 HIS 0.004 0.001 HIS E 146 PHE 0.016 0.001 PHE C 906 TYR 0.023 0.001 TYR A 351 ARG 0.004 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 3.369 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8543 (t80) REVERT: A 335 LEU cc_start: 0.7998 (tt) cc_final: 0.7776 (tt) REVERT: B 52 HIS cc_start: 0.4867 (OUTLIER) cc_final: 0.4645 (t-170) REVERT: C 329 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7822 (t80) REVERT: C 583 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 147 LYS cc_start: 0.5457 (mmtm) cc_final: 0.4685 (mttm) REVERT: F 78 VAL cc_start: 0.5859 (OUTLIER) cc_final: 0.5648 (t) outliers start: 58 outliers final: 40 residues processed: 181 average time/residue: 0.3805 time to fit residues: 118.8169 Evaluate side-chains 171 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 110 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 357 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30381 Z= 0.415 Angle : 0.690 9.772 41340 Z= 0.342 Chirality : 0.048 0.321 4893 Planarity : 0.005 0.068 5277 Dihedral : 8.603 89.117 5322 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 2.87 % Allowed : 15.15 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3663 helix: 0.63 (0.17), residues: 957 sheet: -0.81 (0.19), residues: 720 loop : -2.46 (0.12), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 152 HIS 0.013 0.001 HIS E 146 PHE 0.031 0.002 PHE E 168 TYR 0.025 0.002 TYR A 421 ARG 0.005 0.001 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 120 time to evaluate : 3.771 Fit side-chains REVERT: B 52 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4872 (t-170) REVERT: C 583 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 147 LYS cc_start: 0.5566 (mmtm) cc_final: 0.4846 (mttm) REVERT: E 633 TRP cc_start: 0.6124 (OUTLIER) cc_final: 0.5704 (p90) outliers start: 92 outliers final: 58 residues processed: 204 average time/residue: 0.3452 time to fit residues: 123.2788 Evaluate side-chains 177 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 117 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 633 TRP Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 896 ILE Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 110 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 300 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 222 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30381 Z= 0.220 Angle : 0.605 10.397 41340 Z= 0.296 Chirality : 0.045 0.331 4893 Planarity : 0.004 0.066 5277 Dihedral : 8.009 86.808 5322 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.12 % Favored : 90.85 % Rotamer: Outliers : 1.97 % Allowed : 16.40 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3663 helix: 0.88 (0.17), residues: 957 sheet: -0.77 (0.19), residues: 750 loop : -2.30 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS D 59 PHE 0.021 0.001 PHE E 168 TYR 0.023 0.001 TYR C 473 ARG 0.004 0.000 ARG E1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 127 time to evaluate : 3.376 Fit side-chains REVERT: B 76 MET cc_start: 0.3136 (pmm) cc_final: 0.1974 (tpt) REVERT: D 147 LYS cc_start: 0.5534 (mmtm) cc_final: 0.4799 (mttm) REVERT: E 329 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (t80) REVERT: E 583 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7375 (tm-30) outliers start: 63 outliers final: 50 residues processed: 182 average time/residue: 0.3645 time to fit residues: 115.1337 Evaluate side-chains 169 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 118 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 39 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 2.9990 chunk 142 optimal weight: 0.0470 chunk 212 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30381 Z= 0.277 Angle : 0.627 10.901 41340 Z= 0.305 Chirality : 0.045 0.330 4893 Planarity : 0.004 0.066 5277 Dihedral : 7.757 85.276 5322 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.18 % Favored : 89.79 % Rotamer: Outliers : 2.06 % Allowed : 16.81 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3663 helix: 0.89 (0.17), residues: 957 sheet: -0.76 (0.19), residues: 741 loop : -2.29 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 152 HIS 0.007 0.001 HIS B 52 PHE 0.021 0.001 PHE E 168 TYR 0.023 0.001 TYR C 473 ARG 0.005 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 120 time to evaluate : 3.369 Fit side-chains REVERT: B 76 MET cc_start: 0.3253 (pmm) cc_final: 0.2226 (tpp) REVERT: D 147 LYS cc_start: 0.5555 (mmtm) cc_final: 0.4830 (mttm) REVERT: E 329 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8546 (t80) outliers start: 66 outliers final: 60 residues processed: 178 average time/residue: 0.3492 time to fit residues: 108.8344 Evaluate side-chains 180 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 119 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain F residue 39 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 0.9990 chunk 340 optimal weight: 2.9990 chunk 310 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 199 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 260 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 299 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 330 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 764 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30381 Z= 0.155 Angle : 0.584 11.084 41340 Z= 0.282 Chirality : 0.044 0.341 4893 Planarity : 0.004 0.068 5277 Dihedral : 7.184 82.709 5322 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.44 % Favored : 91.54 % Rotamer: Outliers : 1.62 % Allowed : 17.34 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3663 helix: 1.17 (0.17), residues: 960 sheet: -0.55 (0.19), residues: 738 loop : -2.19 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS B 52 PHE 0.021 0.001 PHE C 168 TYR 0.022 0.001 TYR C 473 ARG 0.005 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 3.378 Fit side-chains REVERT: B 76 MET cc_start: 0.3243 (pmm) cc_final: 0.2346 (tpp) REVERT: C 84 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8101 (mm) REVERT: D 147 LYS cc_start: 0.5542 (mmtm) cc_final: 0.4778 (mttm) outliers start: 52 outliers final: 42 residues processed: 180 average time/residue: 0.3445 time to fit residues: 109.3267 Evaluate side-chains 171 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 1.9990 chunk 350 optimal weight: 0.6980 chunk 213 optimal weight: 0.0040 chunk 166 optimal weight: 0.0670 chunk 243 optimal weight: 20.0000 chunk 367 optimal weight: 20.0000 chunk 338 optimal weight: 0.5980 chunk 292 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30381 Z= 0.145 Angle : 0.567 11.070 41340 Z= 0.274 Chirality : 0.043 0.339 4893 Planarity : 0.004 0.075 5277 Dihedral : 6.779 80.027 5322 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.90 % Favored : 91.07 % Rotamer: Outliers : 1.44 % Allowed : 17.62 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3663 helix: 1.35 (0.18), residues: 960 sheet: -0.55 (0.19), residues: 762 loop : -2.11 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS E 146 PHE 0.020 0.001 PHE C 168 TYR 0.021 0.001 TYR A 473 ARG 0.003 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 3.631 Fit side-chains REVERT: A 517 LEU cc_start: 0.8623 (tp) cc_final: 0.8390 (tt) REVERT: B 76 MET cc_start: 0.3050 (pmm) cc_final: 0.2401 (tpt) REVERT: C 84 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8071 (mm) REVERT: D 147 LYS cc_start: 0.5502 (mmtm) cc_final: 0.4741 (mttm) outliers start: 46 outliers final: 42 residues processed: 183 average time/residue: 0.3533 time to fit residues: 111.8210 Evaluate side-chains 173 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 676 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 867 ASP Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 6.9990 chunk 311 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 301 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN B 41 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.119358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075519 restraints weight = 83731.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078548 restraints weight = 46065.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077548 restraints weight = 27257.079| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30381 Z= 0.352 Angle : 0.654 11.362 41340 Z= 0.321 Chirality : 0.046 0.334 4893 Planarity : 0.005 0.078 5277 Dihedral : 7.141 81.018 5322 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.67 % Favored : 89.27 % Rotamer: Outliers : 1.69 % Allowed : 17.43 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3663 helix: 1.00 (0.17), residues: 957 sheet: -0.73 (0.19), residues: 735 loop : -2.21 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 152 HIS 0.006 0.001 HIS E 146 PHE 0.021 0.002 PHE A 823 TYR 0.022 0.001 TYR A 421 ARG 0.005 0.001 ARG E 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4755.19 seconds wall clock time: 88 minutes 39.59 seconds (5319.59 seconds total)