Starting phenix.real_space_refine on Sun Mar 17 02:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/03_2024/7vtq_32120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/03_2024/7vtq_32120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/03_2024/7vtq_32120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/03_2024/7vtq_32120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/03_2024/7vtq_32120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/03_2024/7vtq_32120_updated.pdb" } resolution = 3.55 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= 0.004 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 636 5.16 5 C 48924 2.51 5 N 13056 2.21 5 O 13932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A GLU 1004": "OE1" <-> "OE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 861": "OE1" <-> "OE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 861": "OE1" <-> "OE2" Residue "D GLU 1004": "OE1" <-> "OE2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 861": "OE1" <-> "OE2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 861": "OE1" <-> "OE2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 861": "OE1" <-> "OE2" Residue "G GLU 1004": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 861": "OE1" <-> "OE2" Residue "I TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 861": "OE1" <-> "OE2" Residue "J PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 861": "OE1" <-> "OE2" Residue "J GLU 1004": "OE1" <-> "OE2" Residue "K PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 861": "OE1" <-> "OE2" Residue "L TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 365": "OE1" <-> "OE2" Residue "L TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 861": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76572 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "B" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "C" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "D" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "E" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "F" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "G" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "H" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "I" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "J" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "K" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "L" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 30.10, per 1000 atoms: 0.39 Number of scatterers: 76572 At special positions: 0 Unit cell: (217.875, 220.365, 158.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 636 16.00 P 24 15.00 O 13932 8.00 N 13056 7.00 C 48924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 955 " - pdb=" SG CYS A 982 " distance=2.04 Simple disulfide: pdb=" SG CYS B 955 " - pdb=" SG CYS B 982 " distance=2.04 Simple disulfide: pdb=" SG CYS C 955 " - pdb=" SG CYS C 982 " distance=2.04 Simple disulfide: pdb=" SG CYS D 955 " - pdb=" SG CYS D 982 " distance=2.04 Simple disulfide: pdb=" SG CYS E 955 " - pdb=" SG CYS E 982 " distance=2.04 Simple disulfide: pdb=" SG CYS F 955 " - pdb=" SG CYS F 982 " distance=2.04 Simple disulfide: pdb=" SG CYS G 955 " - pdb=" SG CYS G 982 " distance=2.04 Simple disulfide: pdb=" SG CYS H 955 " - pdb=" SG CYS H 982 " distance=2.04 Simple disulfide: pdb=" SG CYS I 955 " - pdb=" SG CYS I 982 " distance=2.04 Simple disulfide: pdb=" SG CYS J 955 " - pdb=" SG CYS J 982 " distance=2.04 Simple disulfide: pdb=" SG CYS K 955 " - pdb=" SG CYS K 982 " distance=2.04 Simple disulfide: pdb=" SG CYS L 955 " - pdb=" SG CYS L 982 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.16 Conformation dependent library (CDL) restraints added in 10.8 seconds 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 463 helices and 43 sheets defined 48.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.19 Creating SS restraints... Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 399 through 406 removed outlier: 4.209A pdb=" N PHE A 406 " --> pdb=" O PHE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 423 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 519 through 531 removed outlier: 3.817A pdb=" N TYR A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.933A pdb=" N GLU A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 601 through 615 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 658 through 670 Processing helix chain 'A' and resid 724 through 736 removed outlier: 4.659A pdb=" N SER A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 735 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 762 Processing helix chain 'A' and resid 781 through 793 Processing helix chain 'A' and resid 808 through 819 removed outlier: 3.901A pdb=" N VAL A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 removed outlier: 4.078A pdb=" N GLN A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 removed outlier: 3.578A pdb=" N LYS A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 907 removed outlier: 3.734A pdb=" N SER A 899 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.765A pdb=" N GLY A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 980 through 991 Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 283 through 286 No H-bonds generated for 'chain 'B' and resid 283 through 286' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 354 through 357 No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 371 through 381 Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'B' and resid 399 through 406 removed outlier: 4.225A pdb=" N PHE B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 459 through 475 Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 519 through 531 removed outlier: 3.810A pdb=" N TYR B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 561 removed outlier: 3.938A pdb=" N GLU B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 584 through 594 Processing helix chain 'B' and resid 601 through 615 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 658 through 670 Processing helix chain 'B' and resid 724 through 736 removed outlier: 4.656A pdb=" N SER B 733 " --> pdb=" O GLY B 729 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 735 " --> pdb=" O PHE B 731 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 762 Processing helix chain 'B' and resid 781 through 793 removed outlier: 4.018A pdb=" N PHE B 785 " --> pdb=" O HIS B 781 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 819 removed outlier: 3.863A pdb=" N VAL B 817 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 850 removed outlier: 3.746A pdb=" N GLN B 842 " --> pdb=" O ALA B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.603A pdb=" N LYS B 875 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 907 removed outlier: 3.671A pdb=" N SER B 899 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 933 removed outlier: 3.711A pdb=" N GLY B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 964 Processing helix chain 'B' and resid 980 through 991 Processing helix chain 'B' and resid 1009 through 1021 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 228 through 241 Processing helix chain 'C' and resid 268 through 275 Processing helix chain 'C' and resid 283 through 286 No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 324 through 332 Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 354 through 357 No H-bonds generated for 'chain 'C' and resid 354 through 357' Processing helix chain 'C' and resid 371 through 381 Processing helix chain 'C' and resid 385 through 397 Processing helix chain 'C' and resid 399 through 406 removed outlier: 4.220A pdb=" N PHE C 406 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 482 through 488 Processing helix chain 'C' and resid 519 through 531 removed outlier: 3.791A pdb=" N TYR C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.950A pdb=" N GLU C 561 " --> pdb=" O VAL C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 584 through 594 Processing helix chain 'C' and resid 601 through 615 Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 658 through 670 Processing helix chain 'C' and resid 724 through 736 removed outlier: 4.700A pdb=" N SER C 733 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 735 " --> pdb=" O PHE C 731 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 736 " --> pdb=" O SER C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 762 Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.991A pdb=" N PHE C 785 " --> pdb=" O HIS C 781 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP C 786 " --> pdb=" O GLN C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 819 removed outlier: 3.844A pdb=" N VAL C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 850 removed outlier: 3.710A pdb=" N GLN C 842 " --> pdb=" O ALA C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 876 removed outlier: 3.724A pdb=" N LYS C 875 " --> pdb=" O VAL C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 907 removed outlier: 3.683A pdb=" N SER C 899 " --> pdb=" O ILE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 933 removed outlier: 3.743A pdb=" N GLY C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 979 through 991 Processing helix chain 'C' and resid 1009 through 1021 Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'D' and resid 268 through 275 Processing helix chain 'D' and resid 283 through 286 No H-bonds generated for 'chain 'D' and resid 283 through 286' Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 354 through 357 No H-bonds generated for 'chain 'D' and resid 354 through 357' Processing helix chain 'D' and resid 371 through 381 Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 399 through 406 removed outlier: 4.209A pdb=" N PHE D 406 " --> pdb=" O PHE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 423 Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 459 through 475 Processing helix chain 'D' and resid 482 through 488 Processing helix chain 'D' and resid 492 through 494 No H-bonds generated for 'chain 'D' and resid 492 through 494' Processing helix chain 'D' and resid 519 through 531 removed outlier: 3.817A pdb=" N TYR D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 561 removed outlier: 3.933A pdb=" N GLU D 561 " --> pdb=" O VAL D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 581 Processing helix chain 'D' and resid 584 through 594 Processing helix chain 'D' and resid 601 through 615 Processing helix chain 'D' and resid 625 through 635 Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 658 through 670 Processing helix chain 'D' and resid 724 through 736 removed outlier: 4.659A pdb=" N SER D 733 " --> pdb=" O GLY D 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 734 " --> pdb=" O LEU D 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 735 " --> pdb=" O PHE D 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 762 Processing helix chain 'D' and resid 781 through 793 Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.902A pdb=" N VAL D 817 " --> pdb=" O ARG D 813 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 850 removed outlier: 4.076A pdb=" N GLN D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP D 843 " --> pdb=" O ALA D 839 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 847 " --> pdb=" O ASP D 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 849 " --> pdb=" O ALA D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.578A pdb=" N LYS D 875 " --> pdb=" O VAL D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 907 removed outlier: 3.734A pdb=" N SER D 899 " --> pdb=" O ILE D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 933 removed outlier: 3.765A pdb=" N GLY D 932 " --> pdb=" O LEU D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 964 Processing helix chain 'D' and resid 980 through 991 Processing helix chain 'D' and resid 1009 through 1021 Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 228 through 240 Processing helix chain 'E' and resid 268 through 275 Processing helix chain 'E' and resid 283 through 286 No H-bonds generated for 'chain 'E' and resid 283 through 286' Processing helix chain 'E' and resid 290 through 292 No H-bonds generated for 'chain 'E' and resid 290 through 292' Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 354 through 357 No H-bonds generated for 'chain 'E' and resid 354 through 357' Processing helix chain 'E' and resid 371 through 381 Processing helix chain 'E' and resid 385 through 397 Processing helix chain 'E' and resid 399 through 406 removed outlier: 4.225A pdb=" N PHE E 406 " --> pdb=" O PHE E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 423 Processing helix chain 'E' and resid 429 through 433 Processing helix chain 'E' and resid 438 through 446 Processing helix chain 'E' and resid 459 through 475 Processing helix chain 'E' and resid 482 through 488 Processing helix chain 'E' and resid 519 through 531 removed outlier: 3.810A pdb=" N TYR E 530 " --> pdb=" O ALA E 526 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU E 531 " --> pdb=" O ALA E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 561 removed outlier: 3.942A pdb=" N GLU E 561 " --> pdb=" O VAL E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 581 Processing helix chain 'E' and resid 584 through 594 Processing helix chain 'E' and resid 601 through 615 Processing helix chain 'E' and resid 625 through 635 Processing helix chain 'E' and resid 638 through 645 Processing helix chain 'E' and resid 658 through 670 Processing helix chain 'E' and resid 724 through 736 removed outlier: 4.653A pdb=" N SER E 733 " --> pdb=" O GLY E 729 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 734 " --> pdb=" O LEU E 730 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 735 " --> pdb=" O PHE E 731 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR E 736 " --> pdb=" O SER E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 762 Processing helix chain 'E' and resid 781 through 793 removed outlier: 4.017A pdb=" N PHE E 785 " --> pdb=" O HIS E 781 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP E 786 " --> pdb=" O GLN E 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 819 removed outlier: 3.873A pdb=" N VAL E 817 " --> pdb=" O ARG E 813 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY E 818 " --> pdb=" O LEU E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 838 through 850 removed outlier: 3.747A pdb=" N GLN E 842 " --> pdb=" O ALA E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 876 removed outlier: 3.603A pdb=" N LYS E 875 " --> pdb=" O VAL E 871 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 907 removed outlier: 3.670A pdb=" N SER E 899 " --> pdb=" O ILE E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 922 through 933 removed outlier: 3.714A pdb=" N GLY E 932 " --> pdb=" O LEU E 928 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 964 Processing helix chain 'E' and resid 980 through 991 Processing helix chain 'E' and resid 1009 through 1021 Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 160 through 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 228 through 241 Processing helix chain 'F' and resid 268 through 275 Processing helix chain 'F' and resid 283 through 286 No H-bonds generated for 'chain 'F' and resid 283 through 286' Processing helix chain 'F' and resid 290 through 292 No H-bonds generated for 'chain 'F' and resid 290 through 292' Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 348 through 350 No H-bonds generated for 'chain 'F' and resid 348 through 350' Processing helix chain 'F' and resid 354 through 357 No H-bonds generated for 'chain 'F' and resid 354 through 357' Processing helix chain 'F' and resid 371 through 381 Processing helix chain 'F' and resid 385 through 397 Processing helix chain 'F' and resid 399 through 406 removed outlier: 4.216A pdb=" N PHE F 406 " --> pdb=" O PHE F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 423 Processing helix chain 'F' and resid 429 through 433 Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 459 through 475 Processing helix chain 'F' and resid 482 through 488 Processing helix chain 'F' and resid 492 through 494 No H-bonds generated for 'chain 'F' and resid 492 through 494' Processing helix chain 'F' and resid 519 through 531 removed outlier: 3.787A pdb=" N TYR F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU F 531 " --> pdb=" O ALA F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 561 removed outlier: 3.949A pdb=" N GLU F 561 " --> pdb=" O VAL F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 581 Processing helix chain 'F' and resid 584 through 594 Processing helix chain 'F' and resid 601 through 615 Processing helix chain 'F' and resid 625 through 635 Processing helix chain 'F' and resid 638 through 645 Processing helix chain 'F' and resid 658 through 670 Processing helix chain 'F' and resid 724 through 736 removed outlier: 4.703A pdb=" N SER F 733 " --> pdb=" O GLY F 729 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 734 " --> pdb=" O LEU F 730 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 735 " --> pdb=" O PHE F 731 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR F 736 " --> pdb=" O SER F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 762 Processing helix chain 'F' and resid 781 through 793 removed outlier: 3.990A pdb=" N PHE F 785 " --> pdb=" O HIS F 781 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP F 786 " --> pdb=" O GLN F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 819 removed outlier: 3.844A pdb=" N VAL F 817 " --> pdb=" O ARG F 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY F 818 " --> pdb=" O LEU F 814 " (cutoff:3.500A) Processing helix chain 'F' and resid 838 through 850 removed outlier: 3.710A pdb=" N GLN F 842 " --> pdb=" O ALA F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 876 removed outlier: 3.722A pdb=" N LYS F 875 " --> pdb=" O VAL F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 907 removed outlier: 3.684A pdb=" N SER F 899 " --> pdb=" O ILE F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 922 through 933 removed outlier: 3.744A pdb=" N GLY F 932 " --> pdb=" O LEU F 928 " (cutoff:3.500A) Processing helix chain 'F' and resid 955 through 964 Processing helix chain 'F' and resid 979 through 991 Processing helix chain 'F' and resid 1009 through 1021 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 201 through 203 No H-bonds generated for 'chain 'G' and resid 201 through 203' Processing helix chain 'G' and resid 228 through 241 Processing helix chain 'G' and resid 268 through 275 Processing helix chain 'G' and resid 283 through 286 No H-bonds generated for 'chain 'G' and resid 283 through 286' Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 324 through 332 Processing helix chain 'G' and resid 348 through 350 No H-bonds generated for 'chain 'G' and resid 348 through 350' Processing helix chain 'G' and resid 354 through 357 No H-bonds generated for 'chain 'G' and resid 354 through 357' Processing helix chain 'G' and resid 371 through 381 Processing helix chain 'G' and resid 385 through 397 Processing helix chain 'G' and resid 399 through 406 removed outlier: 4.208A pdb=" N PHE G 406 " --> pdb=" O PHE G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 423 Processing helix chain 'G' and resid 429 through 433 Processing helix chain 'G' and resid 438 through 446 Processing helix chain 'G' and resid 459 through 475 Processing helix chain 'G' and resid 482 through 488 Processing helix chain 'G' and resid 492 through 494 No H-bonds generated for 'chain 'G' and resid 492 through 494' Processing helix chain 'G' and resid 519 through 531 removed outlier: 3.817A pdb=" N TYR G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU G 531 " --> pdb=" O ALA G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 561 removed outlier: 3.933A pdb=" N GLU G 561 " --> pdb=" O VAL G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 581 Processing helix chain 'G' and resid 584 through 594 Processing helix chain 'G' and resid 601 through 615 Processing helix chain 'G' and resid 625 through 635 Processing helix chain 'G' and resid 638 through 645 Processing helix chain 'G' and resid 658 through 670 Processing helix chain 'G' and resid 724 through 736 removed outlier: 4.659A pdb=" N SER G 733 " --> pdb=" O GLY G 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU G 734 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER G 735 " --> pdb=" O PHE G 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR G 736 " --> pdb=" O SER G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 751 through 762 Processing helix chain 'G' and resid 781 through 793 removed outlier: 3.991A pdb=" N PHE G 785 " --> pdb=" O HIS G 781 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP G 786 " --> pdb=" O GLN G 782 " (cutoff:3.500A) Processing helix chain 'G' and resid 808 through 819 removed outlier: 3.901A pdb=" N VAL G 817 " --> pdb=" O ARG G 813 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY G 818 " --> pdb=" O LEU G 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 838 through 850 removed outlier: 4.079A pdb=" N GLN G 842 " --> pdb=" O SER G 838 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP G 843 " --> pdb=" O ALA G 839 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 847 " --> pdb=" O ASP G 843 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER G 849 " --> pdb=" O ALA G 845 " (cutoff:3.500A) Processing helix chain 'G' and resid 865 through 876 removed outlier: 3.578A pdb=" N LYS G 875 " --> pdb=" O VAL G 871 " (cutoff:3.500A) Processing helix chain 'G' and resid 895 through 907 removed outlier: 3.734A pdb=" N SER G 899 " --> pdb=" O ILE G 896 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 933 removed outlier: 3.765A pdb=" N GLY G 932 " --> pdb=" O LEU G 928 " (cutoff:3.500A) Processing helix chain 'G' and resid 955 through 964 Processing helix chain 'G' and resid 980 through 991 Processing helix chain 'G' and resid 1009 through 1021 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'H' and resid 228 through 240 Processing helix chain 'H' and resid 268 through 275 Processing helix chain 'H' and resid 283 through 286 No H-bonds generated for 'chain 'H' and resid 283 through 286' Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 300 through 302 No H-bonds generated for 'chain 'H' and resid 300 through 302' Processing helix chain 'H' and resid 324 through 332 Processing helix chain 'H' and resid 348 through 350 No H-bonds generated for 'chain 'H' and resid 348 through 350' Processing helix chain 'H' and resid 354 through 357 No H-bonds generated for 'chain 'H' and resid 354 through 357' Processing helix chain 'H' and resid 371 through 381 Processing helix chain 'H' and resid 385 through 397 Processing helix chain 'H' and resid 399 through 406 removed outlier: 4.224A pdb=" N PHE H 406 " --> pdb=" O PHE H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 423 Processing helix chain 'H' and resid 429 through 433 Processing helix chain 'H' and resid 438 through 446 Processing helix chain 'H' and resid 459 through 475 Processing helix chain 'H' and resid 482 through 488 Processing helix chain 'H' and resid 519 through 531 removed outlier: 3.827A pdb=" N TYR H 530 " --> pdb=" O ALA H 526 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU H 531 " --> pdb=" O ALA H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 561 removed outlier: 3.941A pdb=" N GLU H 561 " --> pdb=" O VAL H 558 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 581 Processing helix chain 'H' and resid 584 through 594 Processing helix chain 'H' and resid 601 through 615 Processing helix chain 'H' and resid 625 through 635 Processing helix chain 'H' and resid 638 through 645 Processing helix chain 'H' and resid 658 through 670 Processing helix chain 'H' and resid 724 through 736 removed outlier: 4.658A pdb=" N SER H 733 " --> pdb=" O GLY H 729 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU H 734 " --> pdb=" O LEU H 730 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER H 735 " --> pdb=" O PHE H 731 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR H 736 " --> pdb=" O SER H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 751 through 762 Processing helix chain 'H' and resid 781 through 793 removed outlier: 4.017A pdb=" N PHE H 785 " --> pdb=" O HIS H 781 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP H 786 " --> pdb=" O GLN H 782 " (cutoff:3.500A) Processing helix chain 'H' and resid 808 through 819 removed outlier: 3.874A pdb=" N VAL H 817 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY H 818 " --> pdb=" O LEU H 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 838 through 850 removed outlier: 3.747A pdb=" N GLN H 842 " --> pdb=" O ALA H 839 " (cutoff:3.500A) Processing helix chain 'H' and resid 865 through 876 removed outlier: 3.603A pdb=" N LYS H 875 " --> pdb=" O VAL H 871 " (cutoff:3.500A) Processing helix chain 'H' and resid 895 through 907 removed outlier: 3.670A pdb=" N SER H 899 " --> pdb=" O ILE H 896 " (cutoff:3.500A) Processing helix chain 'H' and resid 922 through 933 removed outlier: 3.712A pdb=" N GLY H 932 " --> pdb=" O LEU H 928 " (cutoff:3.500A) Processing helix chain 'H' and resid 955 through 964 Processing helix chain 'H' and resid 980 through 991 Processing helix chain 'H' and resid 1009 through 1021 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 160 through 163 No H-bonds generated for 'chain 'I' and resid 160 through 163' Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'I' and resid 228 through 241 Processing helix chain 'I' and resid 268 through 275 Processing helix chain 'I' and resid 283 through 286 No H-bonds generated for 'chain 'I' and resid 283 through 286' Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 300 through 302 No H-bonds generated for 'chain 'I' and resid 300 through 302' Processing helix chain 'I' and resid 324 through 332 Processing helix chain 'I' and resid 348 through 350 No H-bonds generated for 'chain 'I' and resid 348 through 350' Processing helix chain 'I' and resid 354 through 357 No H-bonds generated for 'chain 'I' and resid 354 through 357' Processing helix chain 'I' and resid 371 through 381 Processing helix chain 'I' and resid 385 through 397 Processing helix chain 'I' and resid 399 through 406 removed outlier: 4.221A pdb=" N PHE I 406 " --> pdb=" O PHE I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 423 Processing helix chain 'I' and resid 429 through 433 Processing helix chain 'I' and resid 438 through 446 Processing helix chain 'I' and resid 459 through 475 Processing helix chain 'I' and resid 482 through 488 Processing helix chain 'I' and resid 492 through 494 No H-bonds generated for 'chain 'I' and resid 492 through 494' Processing helix chain 'I' and resid 519 through 531 removed outlier: 3.782A pdb=" N TYR I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU I 531 " --> pdb=" O ALA I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 561 removed outlier: 3.965A pdb=" N GLU I 561 " --> pdb=" O VAL I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 581 Processing helix chain 'I' and resid 584 through 594 Processing helix chain 'I' and resid 601 through 615 Processing helix chain 'I' and resid 625 through 635 Processing helix chain 'I' and resid 638 through 645 Processing helix chain 'I' and resid 658 through 670 Processing helix chain 'I' and resid 724 through 736 removed outlier: 4.700A pdb=" N SER I 733 " --> pdb=" O GLY I 729 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU I 734 " --> pdb=" O LEU I 730 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER I 735 " --> pdb=" O PHE I 731 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR I 736 " --> pdb=" O SER I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 762 Processing helix chain 'I' and resid 781 through 793 removed outlier: 3.990A pdb=" N PHE I 785 " --> pdb=" O HIS I 781 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP I 786 " --> pdb=" O GLN I 782 " (cutoff:3.500A) Processing helix chain 'I' and resid 808 through 819 removed outlier: 3.842A pdb=" N VAL I 817 " --> pdb=" O ARG I 813 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY I 818 " --> pdb=" O LEU I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 838 through 850 removed outlier: 3.709A pdb=" N GLN I 842 " --> pdb=" O ALA I 839 " (cutoff:3.500A) Processing helix chain 'I' and resid 865 through 876 removed outlier: 3.723A pdb=" N LYS I 875 " --> pdb=" O VAL I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 895 through 907 removed outlier: 3.683A pdb=" N SER I 899 " --> pdb=" O ILE I 896 " (cutoff:3.500A) Processing helix chain 'I' and resid 922 through 933 removed outlier: 3.744A pdb=" N GLY I 932 " --> pdb=" O LEU I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 955 through 964 Processing helix chain 'I' and resid 979 through 991 Processing helix chain 'I' and resid 1009 through 1021 Processing helix chain 'J' and resid 132 through 144 Processing helix chain 'J' and resid 160 through 163 No H-bonds generated for 'chain 'J' and resid 160 through 163' Processing helix chain 'J' and resid 201 through 203 No H-bonds generated for 'chain 'J' and resid 201 through 203' Processing helix chain 'J' and resid 228 through 241 Processing helix chain 'J' and resid 268 through 275 Processing helix chain 'J' and resid 283 through 286 No H-bonds generated for 'chain 'J' and resid 283 through 286' Processing helix chain 'J' and resid 290 through 292 No H-bonds generated for 'chain 'J' and resid 290 through 292' Processing helix chain 'J' and resid 300 through 302 No H-bonds generated for 'chain 'J' and resid 300 through 302' Processing helix chain 'J' and resid 324 through 332 Processing helix chain 'J' and resid 348 through 350 No H-bonds generated for 'chain 'J' and resid 348 through 350' Processing helix chain 'J' and resid 354 through 357 No H-bonds generated for 'chain 'J' and resid 354 through 357' Processing helix chain 'J' and resid 371 through 381 Processing helix chain 'J' and resid 385 through 397 Processing helix chain 'J' and resid 399 through 406 removed outlier: 4.208A pdb=" N PHE J 406 " --> pdb=" O PHE J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 423 Processing helix chain 'J' and resid 429 through 433 Processing helix chain 'J' and resid 438 through 446 Processing helix chain 'J' and resid 459 through 475 Processing helix chain 'J' and resid 482 through 488 Processing helix chain 'J' and resid 492 through 494 No H-bonds generated for 'chain 'J' and resid 492 through 494' Processing helix chain 'J' and resid 519 through 531 removed outlier: 3.817A pdb=" N TYR J 530 " --> pdb=" O ALA J 526 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU J 531 " --> pdb=" O ALA J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 561 removed outlier: 3.933A pdb=" N GLU J 561 " --> pdb=" O VAL J 558 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 581 Processing helix chain 'J' and resid 584 through 594 Processing helix chain 'J' and resid 601 through 615 Processing helix chain 'J' and resid 625 through 635 Processing helix chain 'J' and resid 638 through 645 Processing helix chain 'J' and resid 658 through 670 Processing helix chain 'J' and resid 724 through 736 removed outlier: 4.659A pdb=" N SER J 733 " --> pdb=" O GLY J 729 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 734 " --> pdb=" O LEU J 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 735 " --> pdb=" O PHE J 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR J 736 " --> pdb=" O SER J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 751 through 762 Processing helix chain 'J' and resid 781 through 793 Processing helix chain 'J' and resid 808 through 819 removed outlier: 3.902A pdb=" N VAL J 817 " --> pdb=" O ARG J 813 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY J 818 " --> pdb=" O LEU J 814 " (cutoff:3.500A) Processing helix chain 'J' and resid 838 through 850 removed outlier: 4.076A pdb=" N GLN J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP J 843 " --> pdb=" O ALA J 839 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL J 847 " --> pdb=" O ASP J 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER J 849 " --> pdb=" O ALA J 845 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.578A pdb=" N LYS J 875 " --> pdb=" O VAL J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 907 removed outlier: 3.734A pdb=" N SER J 899 " --> pdb=" O ILE J 896 " (cutoff:3.500A) Processing helix chain 'J' and resid 922 through 933 removed outlier: 3.765A pdb=" N GLY J 932 " --> pdb=" O LEU J 928 " (cutoff:3.500A) Processing helix chain 'J' and resid 955 through 964 Processing helix chain 'J' and resid 980 through 991 Processing helix chain 'J' and resid 1009 through 1021 Processing helix chain 'K' and resid 132 through 144 Processing helix chain 'K' and resid 160 through 163 No H-bonds generated for 'chain 'K' and resid 160 through 163' Processing helix chain 'K' and resid 201 through 203 No H-bonds generated for 'chain 'K' and resid 201 through 203' Processing helix chain 'K' and resid 228 through 240 Processing helix chain 'K' and resid 268 through 275 Processing helix chain 'K' and resid 283 through 286 No H-bonds generated for 'chain 'K' and resid 283 through 286' Processing helix chain 'K' and resid 290 through 292 No H-bonds generated for 'chain 'K' and resid 290 through 292' Processing helix chain 'K' and resid 300 through 302 No H-bonds generated for 'chain 'K' and resid 300 through 302' Processing helix chain 'K' and resid 324 through 332 Processing helix chain 'K' and resid 348 through 350 No H-bonds generated for 'chain 'K' and resid 348 through 350' Processing helix chain 'K' and resid 354 through 357 No H-bonds generated for 'chain 'K' and resid 354 through 357' Processing helix chain 'K' and resid 371 through 381 Processing helix chain 'K' and resid 385 through 397 Processing helix chain 'K' and resid 399 through 406 removed outlier: 4.225A pdb=" N PHE K 406 " --> pdb=" O PHE K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 423 Processing helix chain 'K' and resid 429 through 433 Processing helix chain 'K' and resid 438 through 446 Processing helix chain 'K' and resid 459 through 475 Processing helix chain 'K' and resid 482 through 488 Processing helix chain 'K' and resid 519 through 531 removed outlier: 3.813A pdb=" N TYR K 530 " --> pdb=" O ALA K 526 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU K 531 " --> pdb=" O ALA K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 561 removed outlier: 3.941A pdb=" N GLU K 561 " --> pdb=" O VAL K 558 " (cutoff:3.500A) Processing helix chain 'K' and resid 570 through 581 Processing helix chain 'K' and resid 584 through 594 Processing helix chain 'K' and resid 601 through 615 Processing helix chain 'K' and resid 625 through 635 Processing helix chain 'K' and resid 638 through 645 Processing helix chain 'K' and resid 658 through 670 Processing helix chain 'K' and resid 724 through 736 removed outlier: 4.654A pdb=" N SER K 733 " --> pdb=" O GLY K 729 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU K 734 " --> pdb=" O LEU K 730 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER K 735 " --> pdb=" O PHE K 731 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR K 736 " --> pdb=" O SER K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 751 through 762 Processing helix chain 'K' and resid 781 through 793 removed outlier: 4.017A pdb=" N PHE K 785 " --> pdb=" O HIS K 781 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP K 786 " --> pdb=" O GLN K 782 " (cutoff:3.500A) Processing helix chain 'K' and resid 808 through 819 removed outlier: 3.875A pdb=" N VAL K 817 " --> pdb=" O ARG K 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY K 818 " --> pdb=" O LEU K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 838 through 850 removed outlier: 3.747A pdb=" N GLN K 842 " --> pdb=" O ALA K 839 " (cutoff:3.500A) Processing helix chain 'K' and resid 865 through 876 removed outlier: 3.602A pdb=" N LYS K 875 " --> pdb=" O VAL K 871 " (cutoff:3.500A) Processing helix chain 'K' and resid 895 through 907 removed outlier: 3.671A pdb=" N SER K 899 " --> pdb=" O ILE K 896 " (cutoff:3.500A) Processing helix chain 'K' and resid 922 through 933 removed outlier: 3.741A pdb=" N GLY K 932 " --> pdb=" O LEU K 928 " (cutoff:3.500A) Processing helix chain 'K' and resid 955 through 964 Processing helix chain 'K' and resid 980 through 991 Processing helix chain 'K' and resid 1009 through 1021 Processing helix chain 'L' and resid 132 through 144 Processing helix chain 'L' and resid 160 through 163 No H-bonds generated for 'chain 'L' and resid 160 through 163' Processing helix chain 'L' and resid 201 through 203 No H-bonds generated for 'chain 'L' and resid 201 through 203' Processing helix chain 'L' and resid 228 through 241 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 283 through 286 No H-bonds generated for 'chain 'L' and resid 283 through 286' Processing helix chain 'L' and resid 290 through 292 No H-bonds generated for 'chain 'L' and resid 290 through 292' Processing helix chain 'L' and resid 300 through 302 No H-bonds generated for 'chain 'L' and resid 300 through 302' Processing helix chain 'L' and resid 324 through 332 Processing helix chain 'L' and resid 348 through 350 No H-bonds generated for 'chain 'L' and resid 348 through 350' Processing helix chain 'L' and resid 354 through 357 No H-bonds generated for 'chain 'L' and resid 354 through 357' Processing helix chain 'L' and resid 371 through 381 Processing helix chain 'L' and resid 385 through 397 Processing helix chain 'L' and resid 399 through 406 removed outlier: 4.220A pdb=" N PHE L 406 " --> pdb=" O PHE L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 423 Processing helix chain 'L' and resid 429 through 433 Processing helix chain 'L' and resid 438 through 446 Processing helix chain 'L' and resid 459 through 475 Processing helix chain 'L' and resid 482 through 488 Processing helix chain 'L' and resid 492 through 494 No H-bonds generated for 'chain 'L' and resid 492 through 494' Processing helix chain 'L' and resid 519 through 531 removed outlier: 3.788A pdb=" N TYR L 530 " --> pdb=" O ALA L 526 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU L 531 " --> pdb=" O ALA L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 556 through 561 removed outlier: 3.948A pdb=" N GLU L 561 " --> pdb=" O VAL L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 570 through 581 Processing helix chain 'L' and resid 584 through 594 Processing helix chain 'L' and resid 601 through 615 Processing helix chain 'L' and resid 625 through 635 Processing helix chain 'L' and resid 638 through 645 Processing helix chain 'L' and resid 658 through 670 Processing helix chain 'L' and resid 724 through 736 removed outlier: 4.701A pdb=" N SER L 733 " --> pdb=" O GLY L 729 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU L 734 " --> pdb=" O LEU L 730 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER L 735 " --> pdb=" O PHE L 731 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR L 736 " --> pdb=" O SER L 732 " (cutoff:3.500A) Processing helix chain 'L' and resid 751 through 762 Processing helix chain 'L' and resid 781 through 793 removed outlier: 3.990A pdb=" N PHE L 785 " --> pdb=" O HIS L 781 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP L 786 " --> pdb=" O GLN L 782 " (cutoff:3.500A) Processing helix chain 'L' and resid 808 through 819 removed outlier: 3.843A pdb=" N VAL L 817 " --> pdb=" O ARG L 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 818 " --> pdb=" O LEU L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 838 through 850 removed outlier: 3.729A pdb=" N GLN L 842 " --> pdb=" O ALA L 839 " (cutoff:3.500A) Processing helix chain 'L' and resid 865 through 876 removed outlier: 3.725A pdb=" N LYS L 875 " --> pdb=" O VAL L 871 " (cutoff:3.500A) Processing helix chain 'L' and resid 895 through 907 removed outlier: 3.680A pdb=" N SER L 899 " --> pdb=" O ILE L 896 " (cutoff:3.500A) Processing helix chain 'L' and resid 922 through 933 removed outlier: 3.733A pdb=" N GLY L 932 " --> pdb=" O LEU L 928 " (cutoff:3.500A) Processing helix chain 'L' and resid 955 through 964 Processing helix chain 'L' and resid 979 through 991 Processing helix chain 'L' and resid 1009 through 1021 Processing sheet with id= A, first strand: chain 'A' and resid 168 through 171 removed outlier: 7.012A pdb=" N VAL A 170 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE A 366 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 342 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE A 220 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A 344 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY A 222 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 346 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR A 251 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU A 296 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 253 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP A 298 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE A 255 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 650 through 655 removed outlier: 6.667A pdb=" N THR A 676 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE A 653 " --> pdb=" O THR A 676 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER A 678 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU A 655 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 680 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU A 742 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU A 679 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP A 744 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE A 681 " --> pdb=" O ASP A 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 799 through 801 removed outlier: 6.243A pdb=" N LYS A 828 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG A 856 " --> pdb=" O LEU A 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.994A pdb=" N VAL B 170 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE B 366 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 342 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N PHE B 220 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 344 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLY B 222 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B 346 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR B 251 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LEU B 296 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 253 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP B 298 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE B 255 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 499 through 502 Processing sheet with id= F, first strand: chain 'B' and resid 650 through 655 removed outlier: 6.679A pdb=" N THR B 676 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B 653 " --> pdb=" O THR B 676 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 678 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 655 " --> pdb=" O SER B 678 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 680 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU B 742 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU B 679 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP B 744 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N PHE B 681 " --> pdb=" O ASP B 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 799 through 801 removed outlier: 6.201A pdb=" N LYS B 828 " --> pdb=" O LEU B 800 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B 856 " --> pdb=" O LEU B 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 168 through 171 removed outlier: 7.004A pdb=" N VAL C 170 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE C 366 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU C 342 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N PHE C 220 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 344 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY C 222 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR C 346 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR C 251 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU C 296 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE C 253 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASP C 298 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE C 255 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 499 through 502 Processing sheet with id= J, first strand: chain 'C' and resid 650 through 655 removed outlier: 6.657A pdb=" N THR C 676 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE C 653 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER C 678 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU C 655 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY C 680 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C 742 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU C 679 " --> pdb=" O GLU C 742 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP C 744 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE C 681 " --> pdb=" O ASP C 744 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG C 771 " --> pdb=" O LEU C 743 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 799 through 801 removed outlier: 6.188A pdb=" N LYS C 828 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG C 856 " --> pdb=" O LEU C 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 168 through 171 removed outlier: 7.012A pdb=" N VAL D 170 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE D 366 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 342 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE D 220 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE D 344 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY D 222 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR D 346 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR D 251 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU D 296 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE D 253 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP D 298 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 255 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 650 through 655 removed outlier: 6.666A pdb=" N THR D 676 " --> pdb=" O ILE D 651 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE D 653 " --> pdb=" O THR D 676 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER D 678 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU D 655 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY D 680 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU D 742 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LEU D 679 " --> pdb=" O GLU D 742 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP D 744 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE D 681 " --> pdb=" O ASP D 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 799 through 801 removed outlier: 6.243A pdb=" N LYS D 828 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG D 856 " --> pdb=" O LEU D 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 168 through 171 removed outlier: 6.971A pdb=" N VAL E 170 " --> pdb=" O ILE E 366 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE E 366 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU E 342 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N PHE E 220 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 344 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N GLY E 222 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR E 346 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR E 251 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU E 296 " --> pdb=" O TYR E 251 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE E 253 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASP E 298 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE E 255 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 499 through 502 Processing sheet with id= Q, first strand: chain 'E' and resid 650 through 655 removed outlier: 6.685A pdb=" N THR E 676 " --> pdb=" O ILE E 651 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ILE E 653 " --> pdb=" O THR E 676 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER E 678 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU E 655 " --> pdb=" O SER E 678 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY E 680 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU E 742 " --> pdb=" O LEU E 677 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU E 679 " --> pdb=" O GLU E 742 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP E 744 " --> pdb=" O LEU E 679 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N PHE E 681 " --> pdb=" O ASP E 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 799 through 801 removed outlier: 6.206A pdb=" N LYS E 828 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG E 856 " --> pdb=" O LEU E 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 168 through 171 removed outlier: 6.870A pdb=" N VAL F 170 " --> pdb=" O ILE F 366 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE F 366 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU F 342 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE F 220 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE F 344 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N GLY F 222 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR F 346 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR F 251 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU F 296 " --> pdb=" O TYR F 251 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE F 253 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP F 298 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE F 255 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 499 through 502 Processing sheet with id= U, first strand: chain 'F' and resid 650 through 655 removed outlier: 6.658A pdb=" N THR F 676 " --> pdb=" O ILE F 651 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE F 653 " --> pdb=" O THR F 676 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER F 678 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU F 655 " --> pdb=" O SER F 678 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY F 680 " --> pdb=" O LEU F 655 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU F 742 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU F 679 " --> pdb=" O GLU F 742 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP F 744 " --> pdb=" O LEU F 679 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N PHE F 681 " --> pdb=" O ASP F 744 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG F 771 " --> pdb=" O LEU F 743 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 799 through 801 removed outlier: 6.189A pdb=" N LYS F 828 " --> pdb=" O LEU F 800 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG F 856 " --> pdb=" O LEU F 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 168 through 171 removed outlier: 7.014A pdb=" N VAL G 170 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE G 366 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU G 342 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE G 220 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE G 344 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLY G 222 " --> pdb=" O ILE G 344 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR G 346 " --> pdb=" O GLY G 222 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR G 251 " --> pdb=" O LEU G 294 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU G 296 " --> pdb=" O TYR G 251 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE G 253 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASP G 298 " --> pdb=" O PHE G 253 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE G 255 " --> pdb=" O ASP G 298 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 650 through 655 removed outlier: 6.667A pdb=" N THR G 676 " --> pdb=" O ILE G 651 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE G 653 " --> pdb=" O THR G 676 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER G 678 " --> pdb=" O ILE G 653 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU G 655 " --> pdb=" O SER G 678 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY G 680 " --> pdb=" O LEU G 655 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU G 742 " --> pdb=" O LEU G 677 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU G 679 " --> pdb=" O GLU G 742 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP G 744 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE G 681 " --> pdb=" O ASP G 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 799 through 801 removed outlier: 6.244A pdb=" N LYS G 828 " --> pdb=" O LEU G 800 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG G 856 " --> pdb=" O LEU G 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'H' and resid 168 through 171 removed outlier: 6.992A pdb=" N VAL H 170 " --> pdb=" O ILE H 366 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE H 366 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU H 342 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N PHE H 220 " --> pdb=" O LEU H 342 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE H 344 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLY H 222 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR H 346 " --> pdb=" O GLY H 222 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR H 251 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU H 296 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE H 253 " --> pdb=" O LEU H 296 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP H 298 " --> pdb=" O PHE H 253 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE H 255 " --> pdb=" O ASP H 298 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 499 through 502 Processing sheet with id= AB, first strand: chain 'H' and resid 650 through 655 removed outlier: 6.675A pdb=" N THR H 676 " --> pdb=" O ILE H 651 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ILE H 653 " --> pdb=" O THR H 676 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER H 678 " --> pdb=" O ILE H 653 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU H 655 " --> pdb=" O SER H 678 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY H 680 " --> pdb=" O LEU H 655 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU H 742 " --> pdb=" O LEU H 677 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU H 679 " --> pdb=" O GLU H 742 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP H 744 " --> pdb=" O LEU H 679 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N PHE H 681 " --> pdb=" O ASP H 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 799 through 801 removed outlier: 6.201A pdb=" N LYS H 828 " --> pdb=" O LEU H 800 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG H 856 " --> pdb=" O LEU H 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'I' and resid 168 through 171 removed outlier: 6.948A pdb=" N VAL I 170 " --> pdb=" O ILE I 366 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE I 366 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU I 342 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE I 220 " --> pdb=" O LEU I 342 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE I 344 " --> pdb=" O PHE I 220 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLY I 222 " --> pdb=" O ILE I 344 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR I 346 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR I 251 " --> pdb=" O LEU I 294 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LEU I 296 " --> pdb=" O TYR I 251 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE I 253 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP I 298 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE I 255 " --> pdb=" O ASP I 298 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 499 through 502 Processing sheet with id= AF, first strand: chain 'I' and resid 650 through 655 removed outlier: 6.658A pdb=" N THR I 676 " --> pdb=" O ILE I 651 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE I 653 " --> pdb=" O THR I 676 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER I 678 " --> pdb=" O ILE I 653 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU I 655 " --> pdb=" O SER I 678 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY I 680 " --> pdb=" O LEU I 655 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU I 742 " --> pdb=" O LEU I 677 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU I 679 " --> pdb=" O GLU I 742 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP I 744 " --> pdb=" O LEU I 679 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE I 681 " --> pdb=" O ASP I 744 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG I 771 " --> pdb=" O LEU I 743 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU I 799 " --> pdb=" O LEU I 772 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS I 828 " --> pdb=" O LEU I 800 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG I 856 " --> pdb=" O LEU I 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'J' and resid 168 through 171 removed outlier: 7.014A pdb=" N VAL J 170 " --> pdb=" O ILE J 366 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE J 366 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU J 342 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE J 220 " --> pdb=" O LEU J 342 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE J 344 " --> pdb=" O PHE J 220 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLY J 222 " --> pdb=" O ILE J 344 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR J 346 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR J 251 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU J 296 " --> pdb=" O TYR J 251 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE J 253 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP J 298 " --> pdb=" O PHE J 253 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE J 255 " --> pdb=" O ASP J 298 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 650 through 655 removed outlier: 6.667A pdb=" N THR J 676 " --> pdb=" O ILE J 651 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE J 653 " --> pdb=" O THR J 676 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER J 678 " --> pdb=" O ILE J 653 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU J 655 " --> pdb=" O SER J 678 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY J 680 " --> pdb=" O LEU J 655 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU J 742 " --> pdb=" O LEU J 677 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU J 679 " --> pdb=" O GLU J 742 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP J 744 " --> pdb=" O LEU J 679 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE J 681 " --> pdb=" O ASP J 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'J' and resid 799 through 801 removed outlier: 6.243A pdb=" N LYS J 828 " --> pdb=" O LEU J 800 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG J 856 " --> pdb=" O LEU J 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'K' and resid 168 through 171 removed outlier: 6.972A pdb=" N VAL K 170 " --> pdb=" O ILE K 366 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE K 366 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU K 342 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N PHE K 220 " --> pdb=" O LEU K 342 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE K 344 " --> pdb=" O PHE K 220 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLY K 222 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR K 346 " --> pdb=" O GLY K 222 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR K 251 " --> pdb=" O LEU K 294 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU K 296 " --> pdb=" O TYR K 251 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE K 253 " --> pdb=" O LEU K 296 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP K 298 " --> pdb=" O PHE K 253 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE K 255 " --> pdb=" O ASP K 298 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 499 through 502 Processing sheet with id= AL, first strand: chain 'K' and resid 650 through 655 removed outlier: 6.687A pdb=" N THR K 676 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ILE K 653 " --> pdb=" O THR K 676 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER K 678 " --> pdb=" O ILE K 653 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU K 655 " --> pdb=" O SER K 678 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLY K 680 " --> pdb=" O LEU K 655 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU K 742 " --> pdb=" O LEU K 677 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU K 679 " --> pdb=" O GLU K 742 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP K 744 " --> pdb=" O LEU K 679 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N PHE K 681 " --> pdb=" O ASP K 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'K' and resid 799 through 801 removed outlier: 6.217A pdb=" N LYS K 828 " --> pdb=" O LEU K 800 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG K 856 " --> pdb=" O LEU K 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'L' and resid 168 through 171 removed outlier: 7.008A pdb=" N VAL L 170 " --> pdb=" O ILE L 366 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE L 366 " --> pdb=" O VAL L 170 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU L 342 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N PHE L 220 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE L 344 " --> pdb=" O PHE L 220 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY L 222 " --> pdb=" O ILE L 344 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR L 346 " --> pdb=" O GLY L 222 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR L 251 " --> pdb=" O LEU L 294 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LEU L 296 " --> pdb=" O TYR L 251 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE L 253 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASP L 298 " --> pdb=" O PHE L 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE L 255 " --> pdb=" O ASP L 298 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 499 through 502 Processing sheet with id= AP, first strand: chain 'L' and resid 650 through 655 removed outlier: 6.658A pdb=" N THR L 676 " --> pdb=" O ILE L 651 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE L 653 " --> pdb=" O THR L 676 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER L 678 " --> pdb=" O ILE L 653 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU L 655 " --> pdb=" O SER L 678 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY L 680 " --> pdb=" O LEU L 655 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU L 742 " --> pdb=" O LEU L 677 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU L 679 " --> pdb=" O GLU L 742 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP L 744 " --> pdb=" O LEU L 679 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N PHE L 681 " --> pdb=" O ASP L 744 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG L 771 " --> pdb=" O LEU L 743 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'L' and resid 799 through 801 removed outlier: 6.188A pdb=" N LYS L 828 " --> pdb=" O LEU L 800 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG L 856 " --> pdb=" O LEU L 829 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ 2771 hydrogen bonds defined for protein. 7479 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: 27.91 Time building geometry restraints manager: 27.52 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: 24491 1.34 - 1.46: 16868 1.46 - 1.58: 35825 1.58 - 1.70: 36 1.70 - 1.82: 828 Bond restraints: 78048 Sorted by residual: bond pdb=" C08 7YN G1502 " pdb=" C09 7YN G1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C08 7YN J1502 " pdb=" C09 7YN J1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C08 7YN B1502 " pdb=" C09 7YN B1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C08 7YN H1502 " pdb=" C09 7YN H1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C08 7YN C1502 " pdb=" C09 7YN C1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.00e+01 ... (remaining 78043 not shown) Histogram of bond angle deviations from ideal: 96.29 - 104.17: 722 104.17 - 112.06: 39324 112.06 - 119.94: 30264 119.94 - 127.82: 34353 127.82 - 135.70: 673 Bond angle restraints: 105336 Sorted by residual: angle pdb=" CA CYS J 955 " pdb=" CB CYS J 955 " pdb=" SG CYS J 955 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS D 955 " pdb=" CB CYS D 955 " pdb=" SG CYS D 955 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS G 955 " pdb=" CB CYS G 955 " pdb=" SG CYS G 955 " ideal model delta sigma weight residual 114.40 121.68 -7.28 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CA CYS A 955 " pdb=" CB CYS A 955 " pdb=" SG CYS A 955 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CA CYS C 955 " pdb=" CB CYS C 955 " pdb=" SG CYS C 955 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 9.99e+00 ... (remaining 105331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 44500 26.29 - 52.58: 2286 52.58 - 78.87: 198 78.87 - 105.16: 44 105.16 - 131.45: 24 Dihedral angle restraints: 47052 sinusoidal: 19452 harmonic: 27600 Sorted by residual: dihedral pdb=" CB CYS F 955 " pdb=" SG CYS F 955 " pdb=" SG CYS F 982 " pdb=" CB CYS F 982 " ideal model delta sinusoidal sigma weight residual -86.00 -159.59 73.59 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS C 955 " pdb=" SG CYS C 955 " pdb=" SG CYS C 982 " pdb=" CB CYS C 982 " ideal model delta sinusoidal sigma weight residual -86.00 -159.51 73.51 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS I 955 " pdb=" SG CYS I 955 " pdb=" SG CYS I 982 " pdb=" CB CYS I 982 " ideal model delta sinusoidal sigma weight residual -86.00 -159.47 73.47 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 47049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 8462 0.038 - 0.076: 2723 0.076 - 0.114: 672 0.114 - 0.152: 101 0.152 - 0.190: 18 Chirality restraints: 11976 Sorted by residual: chirality pdb=" CG LEU E 916 " pdb=" CB LEU E 916 " pdb=" CD1 LEU E 916 " pdb=" CD2 LEU E 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CG LEU D 916 " pdb=" CB LEU D 916 " pdb=" CD1 LEU D 916 " pdb=" CD2 LEU D 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 11973 not shown) Planarity restraints: 13116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN E1502 " -0.029 2.00e-02 2.50e+03 5.25e-02 8.97e+01 pdb=" C02 7YN E1502 " -0.017 2.00e-02 2.50e+03 pdb=" C03 7YN E1502 " -0.035 2.00e-02 2.50e+03 pdb=" C04 7YN E1502 " -0.006 2.00e-02 2.50e+03 pdb=" C05 7YN E1502 " -0.026 2.00e-02 2.50e+03 pdb=" C06 7YN E1502 " -0.011 2.00e-02 2.50e+03 pdb=" C07 7YN E1502 " 0.011 2.00e-02 2.50e+03 pdb=" C08 7YN E1502 " 0.062 2.00e-02 2.50e+03 pdb=" C09 7YN E1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN E1502 " -0.040 2.00e-02 2.50e+03 pdb=" C11 7YN E1502 " 0.155 2.00e-02 2.50e+03 pdb=" C12 7YN E1502 " -0.052 2.00e-02 2.50e+03 pdb=" N13 7YN E1502 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN K1502 " -0.030 2.00e-02 2.50e+03 5.25e-02 8.96e+01 pdb=" C02 7YN K1502 " -0.018 2.00e-02 2.50e+03 pdb=" C03 7YN K1502 " -0.035 2.00e-02 2.50e+03 pdb=" C04 7YN K1502 " -0.006 2.00e-02 2.50e+03 pdb=" C05 7YN K1502 " -0.026 2.00e-02 2.50e+03 pdb=" C06 7YN K1502 " -0.011 2.00e-02 2.50e+03 pdb=" C07 7YN K1502 " 0.011 2.00e-02 2.50e+03 pdb=" C08 7YN K1502 " 0.063 2.00e-02 2.50e+03 pdb=" C09 7YN K1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN K1502 " -0.040 2.00e-02 2.50e+03 pdb=" C11 7YN K1502 " 0.155 2.00e-02 2.50e+03 pdb=" C12 7YN K1502 " -0.052 2.00e-02 2.50e+03 pdb=" N13 7YN K1502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN B1502 " 0.029 2.00e-02 2.50e+03 5.18e-02 8.73e+01 pdb=" C02 7YN B1502 " 0.017 2.00e-02 2.50e+03 pdb=" C03 7YN B1502 " 0.035 2.00e-02 2.50e+03 pdb=" C04 7YN B1502 " 0.006 2.00e-02 2.50e+03 pdb=" C05 7YN B1502 " 0.026 2.00e-02 2.50e+03 pdb=" C06 7YN B1502 " 0.011 2.00e-02 2.50e+03 pdb=" C07 7YN B1502 " -0.011 2.00e-02 2.50e+03 pdb=" C08 7YN B1502 " -0.061 2.00e-02 2.50e+03 pdb=" C09 7YN B1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN B1502 " 0.040 2.00e-02 2.50e+03 pdb=" C11 7YN B1502 " -0.153 2.00e-02 2.50e+03 pdb=" C12 7YN B1502 " 0.051 2.00e-02 2.50e+03 pdb=" N13 7YN B1502 " 0.010 2.00e-02 2.50e+03 ... (remaining 13113 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1711 2.69 - 3.24: 77733 3.24 - 3.79: 120761 3.79 - 4.35: 164454 4.35 - 4.90: 261387 Nonbonded interactions: 626046 Sorted by model distance: nonbonded pdb=" O ASP A 301 " pdb=" OH TYR A 570 " model vdw 2.136 2.440 nonbonded pdb=" O ASP D 301 " pdb=" OH TYR D 570 " model vdw 2.136 2.440 nonbonded pdb=" O ASP G 301 " pdb=" OH TYR G 570 " model vdw 2.136 2.440 nonbonded pdb=" O ASP J 301 " pdb=" OH TYR J 570 " model vdw 2.136 2.440 nonbonded pdb=" O ASP H 301 " pdb=" OH TYR H 570 " model vdw 2.140 2.440 ... (remaining 626041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.050 Extract box with map and model: 6.370 Check model and map are aligned: 0.810 Set scattering table: 0.520 Process input model: 160.050 Find NCS groups from input model: 4.060 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 0.190 78048 Z= 0.270 Angle : 0.684 8.376 105336 Z= 0.338 Chirality : 0.040 0.190 11976 Planarity : 0.003 0.053 13116 Dihedral : 15.119 131.446 29040 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.05 % Allowed : 0.22 % Favored : 99.73 % 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: -0.05 (0.09), residues: 9300 helix: 1.13 (0.08), residues: 4548 sheet: -1.43 (0.16), residues: 1188 loop : -0.99 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 474 HIS 0.004 0.001 HIS C 518 PHE 0.040 0.002 PHE C 378 TYR 0.012 0.001 TYR H 630 ARG 0.009 0.000 ARG L1013 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 520 time to evaluate : 6.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 422 MET cc_start: 0.3095 (ptt) cc_final: 0.2848 (ptp) REVERT: F 422 MET cc_start: 0.3071 (ptt) cc_final: 0.2813 (ptp) REVERT: H 422 MET cc_start: 0.3263 (ptt) cc_final: 0.2969 (ptp) REVERT: I 422 MET cc_start: 0.3103 (ptt) cc_final: 0.2843 (ptp) REVERT: L 422 MET cc_start: 0.3078 (ptt) cc_final: 0.2829 (ptp) outliers start: 4 outliers final: 4 residues processed: 524 average time/residue: 0.6563 time to fit residues: 611.7615 Evaluate side-chains 310 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 306 time to evaluate : 6.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain K residue 396 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 0.7980 chunk 709 optimal weight: 8.9990 chunk 393 optimal weight: 0.6980 chunk 242 optimal weight: 5.9990 chunk 478 optimal weight: 0.8980 chunk 379 optimal weight: 20.0000 chunk 733 optimal weight: 7.9990 chunk 283 optimal weight: 0.2980 chunk 446 optimal weight: 10.0000 chunk 546 optimal weight: 60.0000 chunk 849 optimal weight: 20.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 622 GLN K 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 78048 Z= 0.161 Angle : 0.608 13.003 105336 Z= 0.285 Chirality : 0.039 0.352 11976 Planarity : 0.003 0.028 13116 Dihedral : 8.945 134.631 10416 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.65 % Allowed : 6.92 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 9300 helix: 1.47 (0.08), residues: 4440 sheet: -1.39 (0.16), residues: 1212 loop : -0.85 (0.11), residues: 3648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 621 HIS 0.005 0.001 HIS H 518 PHE 0.028 0.001 PHE C 378 TYR 0.016 0.001 TYR I 570 ARG 0.005 0.000 ARG J1013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 354 time to evaluate : 7.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 19 residues processed: 378 average time/residue: 0.6498 time to fit residues: 441.7480 Evaluate side-chains 306 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 287 time to evaluate : 6.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain F residue 635 MET Chi-restraints excluded: chain F residue 872 LEU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 635 MET Chi-restraints excluded: chain I residue 872 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 872 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 472 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 707 optimal weight: 40.0000 chunk 578 optimal weight: 40.0000 chunk 234 optimal weight: 60.0000 chunk 851 optimal weight: 9.9990 chunk 919 optimal weight: 10.0000 chunk 758 optimal weight: 10.0000 chunk 844 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 683 optimal weight: 3.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN B 957 ASN C 600 GLN C 957 ASN C 976 ASN D 600 GLN ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 805 ASN E 957 ASN F 600 GLN F 957 ASN ** G 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 957 ASN ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 805 ASN H 957 ASN I 957 ASN I 976 ASN ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 805 ASN L 957 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 78048 Z= 0.261 Angle : 0.632 11.065 105336 Z= 0.300 Chirality : 0.039 0.308 11976 Planarity : 0.003 0.028 13116 Dihedral : 8.437 132.532 10416 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.97 % Allowed : 8.79 % Favored : 90.24 % 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: 0.13 (0.09), residues: 9300 helix: 1.35 (0.08), residues: 4500 sheet: -1.57 (0.16), residues: 1188 loop : -0.89 (0.11), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 474 HIS 0.006 0.001 HIS H 518 PHE 0.020 0.001 PHE C 378 TYR 0.013 0.001 TYR I 570 ARG 0.004 0.000 ARG H 658 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 297 time to evaluate : 7.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8220 (ppp) cc_final: 0.7961 (tmm) REVERT: B 942 MET cc_start: 0.7389 (tmm) cc_final: 0.6788 (tmm) REVERT: D 635 MET cc_start: 0.8211 (ppp) cc_final: 0.7950 (tmm) REVERT: E 942 MET cc_start: 0.7359 (tmm) cc_final: 0.6786 (tmm) REVERT: G 635 MET cc_start: 0.8189 (ppp) cc_final: 0.7935 (tmm) REVERT: H 942 MET cc_start: 0.7360 (tmm) cc_final: 0.6781 (tmm) REVERT: J 635 MET cc_start: 0.8199 (ppp) cc_final: 0.7945 (tmm) outliers start: 84 outliers final: 31 residues processed: 368 average time/residue: 0.6313 time to fit residues: 425.9200 Evaluate side-chains 296 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 265 time to evaluate : 6.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 635 MET Chi-restraints excluded: chain F residue 763 GLN Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 635 MET Chi-restraints excluded: chain I residue 763 GLN Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 763 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 841 optimal weight: 8.9990 chunk 640 optimal weight: 50.0000 chunk 441 optimal weight: 5.9990 chunk 94 optimal weight: 50.0000 chunk 406 optimal weight: 50.0000 chunk 571 optimal weight: 7.9990 chunk 854 optimal weight: 5.9990 chunk 904 optimal weight: 8.9990 chunk 446 optimal weight: 10.0000 chunk 809 optimal weight: 50.0000 chunk 243 optimal weight: 0.4980 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 957 ASN ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 GLN G 600 GLN G 957 ASN ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 GLN H 957 ASN I 600 GLN J 600 GLN ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 600 GLN L 600 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 78048 Z= 0.201 Angle : 0.608 13.145 105336 Z= 0.281 Chirality : 0.039 0.361 11976 Planarity : 0.003 0.029 13116 Dihedral : 8.179 133.238 10416 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.07 % Allowed : 10.34 % Favored : 88.59 % 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: 0.26 (0.09), residues: 9300 helix: 1.47 (0.08), residues: 4500 sheet: -1.54 (0.16), residues: 1212 loop : -0.80 (0.11), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 474 HIS 0.005 0.001 HIS H 518 PHE 0.014 0.001 PHE C 378 TYR 0.008 0.001 TYR I 570 ARG 0.003 0.000 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 305 time to evaluate : 6.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8189 (ppp) cc_final: 0.7926 (tmm) REVERT: C 635 MET cc_start: 0.7952 (ppp) cc_final: 0.7696 (tmm) REVERT: D 635 MET cc_start: 0.8181 (ppp) cc_final: 0.7919 (tmm) REVERT: G 635 MET cc_start: 0.8159 (ppp) cc_final: 0.7908 (tmm) REVERT: J 635 MET cc_start: 0.8171 (ppp) cc_final: 0.7915 (tmm) outliers start: 92 outliers final: 34 residues processed: 388 average time/residue: 0.6400 time to fit residues: 453.1941 Evaluate side-chains 302 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 6.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 635 MET Chi-restraints excluded: chain F residue 763 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 635 MET Chi-restraints excluded: chain I residue 763 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 763 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 2.9990 chunk 513 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 673 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 772 optimal weight: 20.0000 chunk 625 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 461 optimal weight: 9.9990 chunk 812 optimal weight: 50.0000 chunk 228 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 957 ASN ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 78048 Z= 0.194 Angle : 0.615 11.092 105336 Z= 0.284 Chirality : 0.040 0.393 11976 Planarity : 0.003 0.030 13116 Dihedral : 7.852 133.439 10404 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.30 % Allowed : 11.17 % Favored : 87.53 % 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: 0.36 (0.09), residues: 9300 helix: 1.53 (0.08), residues: 4488 sheet: -1.46 (0.16), residues: 1188 loop : -0.74 (0.11), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 474 HIS 0.004 0.001 HIS H 518 PHE 0.016 0.001 PHE L 640 TYR 0.009 0.001 TYR I 570 ARG 0.004 0.000 ARG K 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 303 time to evaluate : 6.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 53 residues processed: 405 average time/residue: 0.6328 time to fit residues: 468.4666 Evaluate side-chains 329 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 7.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 630 TYR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 630 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 635 MET Chi-restraints excluded: chain F residue 763 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 760 GLU Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 635 MET Chi-restraints excluded: chain I residue 763 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 760 GLU Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 630 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 344 ILE Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 763 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 304 optimal weight: 20.0000 chunk 814 optimal weight: 40.0000 chunk 178 optimal weight: 30.0000 chunk 531 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 905 optimal weight: 20.0000 chunk 751 optimal weight: 5.9990 chunk 419 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 chunk 475 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 ASN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 ASN ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 957 ASN ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 78048 Z= 0.205 Angle : 0.633 13.106 105336 Z= 0.293 Chirality : 0.041 0.410 11976 Planarity : 0.003 0.031 13116 Dihedral : 7.752 133.176 10404 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.95 % Allowed : 12.62 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.09), residues: 9300 helix: 1.46 (0.08), residues: 4476 sheet: -1.48 (0.16), residues: 1188 loop : -0.73 (0.11), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 609 HIS 0.004 0.001 HIS H 518 PHE 0.013 0.001 PHE L 640 TYR 0.013 0.001 TYR K 132 ARG 0.004 0.000 ARG H 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 294 time to evaluate : 6.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 135 MET cc_start: 0.5327 (ppp) cc_final: 0.5021 (ppp) REVERT: F 135 MET cc_start: 0.4689 (ppp) cc_final: 0.4488 (ppp) REVERT: I 135 MET cc_start: 0.4751 (ppp) cc_final: 0.4538 (ppp) REVERT: K 135 MET cc_start: 0.5290 (ppp) cc_final: 0.4989 (ppp) REVERT: L 135 MET cc_start: 0.4754 (ppp) cc_final: 0.4549 (ppp) outliers start: 82 outliers final: 49 residues processed: 365 average time/residue: 0.6254 time to fit residues: 417.3168 Evaluate side-chains 329 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 280 time to evaluate : 6.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 630 TYR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 630 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 635 MET Chi-restraints excluded: chain F residue 763 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 635 MET Chi-restraints excluded: chain I residue 763 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 760 GLU Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 630 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 763 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 873 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 515 optimal weight: 6.9990 chunk 661 optimal weight: 8.9990 chunk 512 optimal weight: 4.9990 chunk 762 optimal weight: 9.9990 chunk 505 optimal weight: 8.9990 chunk 902 optimal weight: 20.0000 chunk 564 optimal weight: 8.9990 chunk 550 optimal weight: 10.0000 chunk 416 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 ASN ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 ASN F 957 ASN ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 502 ASN ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 957 ASN ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 78048 Z= 0.247 Angle : 0.658 14.489 105336 Z= 0.310 Chirality : 0.041 0.398 11976 Planarity : 0.003 0.031 13116 Dihedral : 7.669 132.674 10404 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.81 % Allowed : 13.44 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 9300 helix: 1.29 (0.08), residues: 4524 sheet: -1.82 (0.15), residues: 1308 loop : -0.60 (0.11), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 609 HIS 0.004 0.001 HIS L 781 PHE 0.011 0.001 PHE B 640 TYR 0.028 0.001 TYR H 132 ARG 0.008 0.000 ARG D 756 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 286 time to evaluate : 7.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 51 residues processed: 345 average time/residue: 0.6391 time to fit residues: 401.5817 Evaluate side-chains 331 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 280 time to evaluate : 6.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 630 TYR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 630 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 635 MET Chi-restraints excluded: chain F residue 763 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 635 MET Chi-restraints excluded: chain I residue 763 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 760 GLU Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 630 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 344 ILE Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 763 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 558 optimal weight: 40.0000 chunk 360 optimal weight: 30.0000 chunk 538 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 573 optimal weight: 40.0000 chunk 614 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 709 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 ASN ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 957 ASN ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 78048 Z= 0.244 Angle : 0.667 15.054 105336 Z= 0.314 Chirality : 0.042 0.378 11976 Planarity : 0.003 0.032 13116 Dihedral : 7.627 132.791 10404 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.93 % Allowed : 13.64 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.09), residues: 9300 helix: 1.24 (0.08), residues: 4548 sheet: -1.57 (0.16), residues: 1188 loop : -0.78 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 609 HIS 0.004 0.001 HIS B 781 PHE 0.012 0.001 PHE E 640 TYR 0.022 0.001 TYR J 132 ARG 0.005 0.000 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 289 time to evaluate : 7.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.4863 (ppp) cc_final: 0.4319 (ppp) REVERT: D 135 MET cc_start: 0.4852 (ppp) cc_final: 0.4316 (ppp) REVERT: G 135 MET cc_start: 0.4939 (ppp) cc_final: 0.4421 (ppp) REVERT: J 135 MET cc_start: 0.4927 (ppp) cc_final: 0.4414 (ppp) outliers start: 80 outliers final: 57 residues processed: 355 average time/residue: 0.6355 time to fit residues: 410.0729 Evaluate side-chains 338 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 281 time to evaluate : 6.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 630 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 396 GLN Chi-restraints excluded: chain F residue 763 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 396 GLN Chi-restraints excluded: chain I residue 763 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 611 GLU Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 344 ILE Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 630 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 344 ILE Chi-restraints excluded: chain L residue 396 GLN Chi-restraints excluded: chain L residue 635 MET Chi-restraints excluded: chain L residue 763 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 820 optimal weight: 5.9990 chunk 864 optimal weight: 0.4980 chunk 788 optimal weight: 0.0010 chunk 840 optimal weight: 5.9990 chunk 506 optimal weight: 6.9990 chunk 366 optimal weight: 7.9990 chunk 660 optimal weight: 30.0000 chunk 257 optimal weight: 0.1980 chunk 759 optimal weight: 8.9990 chunk 795 optimal weight: 20.0000 chunk 837 optimal weight: 5.9990 overall best weight: 2.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 976 ASN ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 976 ASN ** I 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 502 ASN K 957 ASN ** K 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 976 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 78048 Z= 0.152 Angle : 0.644 14.109 105336 Z= 0.295 Chirality : 0.041 0.401 11976 Planarity : 0.003 0.033 13116 Dihedral : 7.467 133.714 10404 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.74 % Allowed : 13.96 % Favored : 85.29 % 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: 0.24 (0.09), residues: 9300 helix: 1.36 (0.08), residues: 4536 sheet: -1.59 (0.16), residues: 1212 loop : -0.67 (0.11), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 474 HIS 0.003 0.001 HIS E 488 PHE 0.013 0.001 PHE J 392 TYR 0.010 0.001 TYR H 530 ARG 0.008 0.000 ARG D 756 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 324 time to evaluate : 6.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5350 (ppp) cc_final: 0.4795 (ppp) REVERT: D 135 MET cc_start: 0.5340 (ppp) cc_final: 0.4794 (ppp) REVERT: E 404 MET cc_start: 0.7727 (mtm) cc_final: 0.7363 (mtt) REVERT: G 135 MET cc_start: 0.5357 (ppp) cc_final: 0.4809 (ppp) REVERT: J 135 MET cc_start: 0.5348 (ppp) cc_final: 0.4804 (ppp) REVERT: K 404 MET cc_start: 0.7675 (mtm) cc_final: 0.7307 (mtt) outliers start: 64 outliers final: 47 residues processed: 381 average time/residue: 0.6334 time to fit residues: 439.9584 Evaluate side-chains 336 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 289 time to evaluate : 6.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 630 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 396 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 396 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 630 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 344 ILE Chi-restraints excluded: chain L residue 396 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 552 optimal weight: 50.0000 chunk 888 optimal weight: 50.0000 chunk 542 optimal weight: 4.9990 chunk 421 optimal weight: 1.9990 chunk 617 optimal weight: 8.9990 chunk 932 optimal weight: 3.9990 chunk 858 optimal weight: 60.0000 chunk 742 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 573 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 957 ASN ** K 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 78048 Z= 0.177 Angle : 0.668 14.194 105336 Z= 0.307 Chirality : 0.042 0.418 11976 Planarity : 0.003 0.033 13116 Dihedral : 7.345 133.001 10404 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.68 % Allowed : 14.26 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 9300 helix: 1.30 (0.08), residues: 4536 sheet: -1.61 (0.16), residues: 1200 loop : -0.49 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP E 621 HIS 0.004 0.001 HIS H 518 PHE 0.012 0.001 PHE D 392 TYR 0.014 0.001 TYR K 132 ARG 0.004 0.000 ARG I 586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 292 time to evaluate : 6.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5193 (ppp) cc_final: 0.4640 (ppp) REVERT: D 135 MET cc_start: 0.5185 (ppp) cc_final: 0.4642 (ppp) REVERT: E 404 MET cc_start: 0.7802 (mtm) cc_final: 0.7560 (mtt) REVERT: G 135 MET cc_start: 0.5442 (ppp) cc_final: 0.4898 (ppp) REVERT: J 135 MET cc_start: 0.5434 (ppp) cc_final: 0.4892 (ppp) REVERT: K 404 MET cc_start: 0.7829 (mtm) cc_final: 0.7577 (mtt) outliers start: 59 outliers final: 47 residues processed: 344 average time/residue: 0.6420 time to fit residues: 402.3720 Evaluate side-chains 339 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 292 time to evaluate : 6.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 630 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 396 GLN Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 396 GLN Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 630 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 344 ILE Chi-restraints excluded: chain L residue 396 GLN Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 589 optimal weight: 0.1980 chunk 790 optimal weight: 0.0470 chunk 227 optimal weight: 5.9990 chunk 684 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 206 optimal weight: 9.9990 chunk 743 optimal weight: 0.2980 chunk 311 optimal weight: 5.9990 chunk 763 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 805 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 805 ASN H 805 ASN ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 805 ASN K 957 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.063021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.046488 restraints weight = 592282.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.047869 restraints weight = 305863.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.048608 restraints weight = 197549.552| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 78048 Z= 0.146 Angle : 0.661 14.720 105336 Z= 0.300 Chirality : 0.041 0.411 11976 Planarity : 0.003 0.033 13116 Dihedral : 7.092 134.163 10404 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.56 % Allowed : 14.42 % Favored : 85.03 % 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: 0.39 (0.09), residues: 9300 helix: 1.35 (0.08), residues: 4560 sheet: -1.14 (0.17), residues: 1068 loop : -0.62 (0.11), residues: 3672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 621 HIS 0.005 0.000 HIS I 764 PHE 0.014 0.001 PHE D 392 TYR 0.016 0.001 TYR I 132 ARG 0.009 0.000 ARG E 756 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10785.52 seconds wall clock time: 197 minutes 7.26 seconds (11827.26 seconds total)