Starting phenix.real_space_refine on Fri Aug 9 22:48:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/08_2024/7q9k_13872.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/08_2024/7q9k_13872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/08_2024/7q9k_13872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/08_2024/7q9k_13872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/08_2024/7q9k_13872.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/08_2024/7q9k_13872.cif" } resolution = 4.5 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 17312 2.51 5 N 4453 2.21 5 O 5341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27225 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7336 Classifications: {'peptide': 943} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7819 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7646 Classifications: {'peptide': 979} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 931} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.73, per 1000 atoms: 0.58 Number of scatterers: 27225 At special positions: 0 Unit cell: (140.22, 141.04, 205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 5341 8.00 N 4453 7.00 C 17312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 328 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 706 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 328 " " NAG B1305 " - " ASN B 600 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 706 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 279 " " NAG C1304 " - " ASN C 328 " " NAG C1305 " - " ASN C 600 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C 654 " " NAG C1308 " - " ASN C 706 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C 714 " " NAG T 1 " - " ASN C 798 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 13.26 Conformation dependent library (CDL) restraints added in 4.8 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 49 sheets defined 24.2% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER A 755 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.594A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.771A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.071A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.898A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.362A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER B 755 " --> pdb=" O GLN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.595A pdb=" N ASN B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.068A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.896A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 405' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER C 755 " --> pdb=" O GLN C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.597A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.069A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.898A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.602A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.744A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.742A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.747A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.590A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 101 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.387A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.560A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.329A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 101 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.385A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC4, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.559A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.893A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.645A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AD8, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.955A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.558A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.492A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3162 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: 12.88 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.35: 8616 1.35 - 1.51: 8406 1.51 - 1.67: 10655 1.67 - 1.83: 153 Bond restraints: 27831 Sorted by residual: bond pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 1.331 1.020 0.311 1.05e-02 9.07e+03 8.78e+02 bond pdb=" C TYR D 104 " pdb=" O TYR D 104 " ideal model delta sigma weight residual 1.233 1.346 -0.113 1.21e-02 6.83e+03 8.76e+01 bond pdb=" C TYR H 104 " pdb=" O TYR H 104 " ideal model delta sigma weight residual 1.233 1.345 -0.112 1.21e-02 6.83e+03 8.56e+01 bond pdb=" N PRO B 524 " pdb=" CD PRO B 524 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" CA TYR H 104 " pdb=" C TYR H 104 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.30e-02 5.92e+03 6.63e+00 ... (remaining 27826 not shown) Histogram of bond angle deviations from ideal: 46.89 - 67.91: 2 67.91 - 88.93: 0 88.93 - 109.95: 4598 109.95 - 130.98: 33181 130.98 - 152.00: 80 Bond angle restraints: 37861 Sorted by residual: angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 122.48 49.07 73.41 1.25e+00 6.40e-01 3.45e+03 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 116.84 46.89 69.95 1.71e+00 3.42e-01 1.67e+03 angle pdb=" O ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 122.59 152.00 -29.41 1.33e+00 5.65e-01 4.89e+02 angle pdb=" CA LYS A 525 " pdb=" C LYS A 525 " pdb=" N LYS A 526 " ideal model delta sigma weight residual 115.78 98.22 17.56 1.35e+00 5.49e-01 1.69e+02 angle pdb=" C LYS A 525 " pdb=" N LYS A 526 " pdb=" CA LYS A 526 " ideal model delta sigma weight residual 121.54 99.60 21.94 1.91e+00 2.74e-01 1.32e+02 ... (remaining 37856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16429 17.85 - 35.71: 604 35.71 - 53.56: 152 53.56 - 71.41: 75 71.41 - 89.27: 20 Dihedral angle restraints: 17280 sinusoidal: 7458 harmonic: 9822 Sorted by residual: dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1040 " pdb=" CB CYS B1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.36 77.36 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.34 77.34 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 17277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4022 0.088 - 0.176: 423 0.176 - 0.264: 6 0.264 - 0.352: 7 0.352 - 0.439: 2 Chirality restraints: 4460 Sorted by residual: chirality pdb=" CA ASN A 328 " pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CB ASN A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4457 not shown) Planarity restraints: 4849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 525 " -0.075 2.00e-02 2.50e+03 1.62e-01 2.61e+02 pdb=" C LYS A 525 " 0.279 2.00e-02 2.50e+03 pdb=" O LYS A 525 " -0.119 2.00e-02 2.50e+03 pdb=" N LYS A 526 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 328 " 0.125 2.00e-02 2.50e+03 1.33e-01 2.23e+02 pdb=" CG ASN C 328 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 328 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 328 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 328 " -0.016 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C ASN A 328 " -0.157 2.00e-02 2.50e+03 pdb=" O ASN A 328 " 0.071 2.00e-02 2.50e+03 pdb=" N ILE A 329 " 0.102 2.00e-02 2.50e+03 ... (remaining 4846 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 12 2.14 - 2.83: 8211 2.83 - 3.52: 34867 3.52 - 4.21: 65473 4.21 - 4.90: 112251 Nonbonded interactions: 220814 Sorted by model distance: nonbonded pdb=" CB PRO B 518 " pdb=" OH TYR C 200 " model vdw 1.447 3.440 nonbonded pdb=" CB ASN A 328 " pdb=" N ILE A 329 " model vdw 1.680 2.816 nonbonded pdb=" O ASN A 328 " pdb=" CA ILE A 329 " model vdw 1.849 2.776 nonbonded pdb=" CG PRO B 518 " pdb=" CZ TYR C 200 " model vdw 1.927 3.660 nonbonded pdb=" CG PRO B 518 " pdb=" CE1 TYR C 200 " model vdw 1.952 3.740 ... (remaining 220809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 439 or resid 499 through 1144 or resid 1301 thr \ ough 1310)) selection = (chain 'C' and (resid 27 through 439 or resid 499 through 1144 or resid 1301 thr \ ough 1310)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 79.240 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.190 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.311 27831 Z= 0.316 Angle : 0.879 73.409 37861 Z= 0.541 Chirality : 0.050 0.439 4460 Planarity : 0.005 0.162 4804 Dihedral : 11.189 89.267 10845 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.73 % Favored : 95.91 % Rotamer: Outliers : 0.44 % Allowed : 2.15 % Favored : 97.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.73 % 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 (0.14), residues: 3328 helix: 0.67 (0.19), residues: 660 sheet: 0.45 (0.16), residues: 913 loop : -0.25 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 50 HIS 0.005 0.001 HIS C1045 PHE 0.016 0.001 PHE B 55 TYR 0.018 0.002 TYR D 33 ARG 0.005 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 378 time to evaluate : 3.031 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: 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 1092 PHE cc_start: 0.4942 (m-80) cc_final: 0.4157 (m-80) REVERT: B 37 TYR cc_start: 0.6585 (p90) cc_final: 0.6201 (p90) REVERT: B 49 HIS cc_start: 0.8914 (t70) cc_final: 0.8507 (t70) REVERT: B 711 ILE cc_start: 0.7722 (mt) cc_final: 0.7521 (tt) REVERT: B 745 GLU cc_start: 0.8714 (mp0) cc_final: 0.8150 (tm-30) REVERT: B 767 ILE cc_start: 0.9390 (mt) cc_final: 0.8819 (pt) REVERT: B 770 GLU cc_start: 0.8964 (pt0) cc_final: 0.8696 (pp20) REVERT: C 55 PHE cc_start: 0.9124 (m-80) cc_final: 0.8220 (m-80) REVERT: C 744 THR cc_start: 0.9401 (m) cc_final: 0.9101 (p) REVERT: C 1106 PHE cc_start: 0.9221 (t80) cc_final: 0.8992 (t80) REVERT: L 4 MET cc_start: 0.8379 (mmm) cc_final: 0.7985 (mmm) REVERT: D 81 MET cc_start: 0.4418 (tmm) cc_final: 0.3288 (ppp) outliers start: 13 outliers final: 4 residues processed: 389 average time/residue: 0.4409 time to fit residues: 260.6673 Evaluate side-chains 203 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 304 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 999 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN B 87 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 801 GLN B 869 GLN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 954 GLN B 999 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN B1116 ASN C 748 ASN ** C 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN C 916 ASN C1007 GLN C1051 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN H 117 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 27831 Z= 0.365 Angle : 0.805 13.931 37861 Z= 0.420 Chirality : 0.050 0.328 4460 Planarity : 0.005 0.081 4804 Dihedral : 6.686 56.996 4879 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Rotamer: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: -0.02 (0.14), residues: 3328 helix: 0.71 (0.20), residues: 661 sheet: 0.24 (0.16), residues: 904 loop : -0.36 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.010 0.002 HIS B1061 PHE 0.032 0.003 PHE B1100 TYR 0.045 0.003 TYR A 200 ARG 0.022 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 238 time to evaluate : 3.316 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.9324 (tpt) cc_final: 0.9045 (tpp) REVERT: A 897 MET cc_start: 0.7534 (mmt) cc_final: 0.7276 (mmt) REVERT: A 993 LEU cc_start: 0.9408 (pp) cc_final: 0.9107 (mm) REVERT: A 1064 TYR cc_start: 0.8166 (t80) cc_final: 0.7072 (t80) REVERT: B 37 TYR cc_start: 0.7884 (p90) cc_final: 0.7539 (p90) REVERT: B 745 GLU cc_start: 0.8854 (mp0) cc_final: 0.8475 (tt0) REVERT: B 861 LEU cc_start: 0.9120 (tp) cc_final: 0.8872 (tp) REVERT: C 331 ASN cc_start: 0.9106 (t0) cc_final: 0.8820 (p0) REVERT: C 753 TYR cc_start: 0.7596 (m-80) cc_final: 0.7201 (m-80) REVERT: C 914 TYR cc_start: 0.7196 (m-80) cc_final: 0.6751 (m-10) REVERT: C 915 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8783 (mp0) REVERT: C 982 ASP cc_start: 0.8924 (p0) cc_final: 0.8540 (p0) REVERT: C 985 GLU cc_start: 0.9098 (pt0) cc_final: 0.8520 (pm20) REVERT: C 989 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8405 (mm-40) REVERT: H 81 MET cc_start: 0.3634 (mmm) cc_final: 0.2522 (mmm) outliers start: 4 outliers final: 1 residues processed: 241 average time/residue: 0.4110 time to fit residues: 154.4704 Evaluate side-chains 154 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 304 optimal weight: 0.0370 chunk 329 optimal weight: 50.0000 chunk 271 optimal weight: 5.9990 chunk 302 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27831 Z= 0.276 Angle : 0.642 11.013 37861 Z= 0.336 Chirality : 0.047 0.777 4460 Planarity : 0.005 0.080 4804 Dihedral : 6.052 59.879 4879 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.09 (0.14), residues: 3328 helix: 0.92 (0.20), residues: 657 sheet: 0.25 (0.16), residues: 885 loop : -0.29 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.010 0.002 HIS B1085 PHE 0.023 0.002 PHE A 715 TYR 0.031 0.002 TYR A1064 ARG 0.009 0.001 ARG B 980 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.230 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: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.9349 (tpt) cc_final: 0.9130 (tpp) REVERT: A 1064 TYR cc_start: 0.8253 (t80) cc_final: 0.7625 (t80) REVERT: B 37 TYR cc_start: 0.7954 (p90) cc_final: 0.7709 (p90) REVERT: B 858 LEU cc_start: 0.9171 (tp) cc_final: 0.8945 (tp) REVERT: B 982 ASP cc_start: 0.8519 (p0) cc_final: 0.8319 (p0) REVERT: B 1107 TYR cc_start: 0.8408 (t80) cc_final: 0.7973 (t80) REVERT: B 1110 GLN cc_start: 0.8656 (pt0) cc_final: 0.8408 (pm20) REVERT: C 331 ASN cc_start: 0.9190 (t0) cc_final: 0.8906 (p0) REVERT: C 753 TYR cc_start: 0.7857 (m-80) cc_final: 0.7284 (m-80) REVERT: C 914 TYR cc_start: 0.6652 (m-80) cc_final: 0.6362 (m-10) REVERT: C 982 ASP cc_start: 0.9005 (p0) cc_final: 0.8780 (p0) REVERT: C 985 GLU cc_start: 0.9068 (pt0) cc_final: 0.8522 (pm20) REVERT: C 1047 MET cc_start: 0.9271 (tpt) cc_final: 0.8870 (tpt) REVERT: D 48 MET cc_start: 0.5033 (ttp) cc_final: 0.4528 (tmm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3952 time to fit residues: 137.9745 Evaluate side-chains 143 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 20.0000 chunk 229 optimal weight: 40.0000 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 204 optimal weight: 0.0980 chunk 305 optimal weight: 50.0000 chunk 323 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 289 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN C 916 ASN C 989 GLN C 999 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN H 117 GLN L 89 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27831 Z= 0.203 Angle : 0.582 9.264 37861 Z= 0.304 Chirality : 0.046 0.661 4460 Planarity : 0.004 0.062 4804 Dihedral : 5.444 53.285 4879 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.01 (0.14), residues: 3328 helix: 0.87 (0.20), residues: 656 sheet: 0.15 (0.16), residues: 912 loop : -0.32 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A1061 PHE 0.022 0.001 PHE B1100 TYR 0.022 0.001 TYR A1004 ARG 0.009 0.001 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 3.471 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: A 737 MET cc_start: 0.9342 (tpt) cc_final: 0.9074 (tpp) REVERT: A 1064 TYR cc_start: 0.8553 (t80) cc_final: 0.8092 (t80) REVERT: B 37 TYR cc_start: 0.7996 (p90) cc_final: 0.7757 (p90) REVERT: B 607 VAL cc_start: 0.8959 (m) cc_final: 0.8735 (m) REVERT: B 711 ILE cc_start: 0.9163 (mt) cc_final: 0.8881 (mp) REVERT: B 961 LYS cc_start: 0.9474 (ptpp) cc_final: 0.9256 (ptpp) REVERT: B 982 ASP cc_start: 0.8558 (p0) cc_final: 0.8329 (p0) REVERT: B 1004 TYR cc_start: 0.9445 (t80) cc_final: 0.9197 (t80) REVERT: B 1099 TRP cc_start: 0.8862 (m100) cc_final: 0.8536 (m100) REVERT: B 1107 TYR cc_start: 0.8400 (t80) cc_final: 0.7994 (t80) REVERT: B 1110 GLN cc_start: 0.8717 (pt0) cc_final: 0.8489 (pm20) REVERT: C 331 ASN cc_start: 0.9241 (t0) cc_final: 0.8983 (p0) REVERT: C 760 LEU cc_start: 0.9525 (mt) cc_final: 0.9010 (mt) REVERT: C 914 TYR cc_start: 0.6689 (m-80) cc_final: 0.6448 (m-10) REVERT: C 1016 ARG cc_start: 0.8915 (tpt-90) cc_final: 0.8676 (tpp80) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.3868 time to fit residues: 130.3324 Evaluate side-chains 146 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 276 optimal weight: 0.9990 chunk 223 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 40.0000 chunk 290 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN B 87 ASN B 196 ASN ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27831 Z= 0.149 Angle : 0.534 9.445 37861 Z= 0.276 Chirality : 0.045 0.528 4460 Planarity : 0.004 0.059 4804 Dihedral : 5.044 53.455 4879 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.20 (0.14), residues: 3328 helix: 1.18 (0.20), residues: 674 sheet: 0.23 (0.16), residues: 928 loop : -0.26 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS C1045 PHE 0.029 0.001 PHE A 756 TYR 0.024 0.001 TYR A1064 ARG 0.011 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 3.482 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: A 737 MET cc_start: 0.9282 (tpt) cc_final: 0.9059 (tpp) REVERT: A 1092 PHE cc_start: 0.6275 (m-10) cc_final: 0.5238 (m-80) REVERT: B 711 ILE cc_start: 0.9079 (mt) cc_final: 0.8702 (mp) REVERT: B 728 MET cc_start: 0.8327 (ppp) cc_final: 0.7781 (ppp) REVERT: B 861 LEU cc_start: 0.8973 (mm) cc_final: 0.8541 (mm) REVERT: B 866 MET cc_start: 0.9178 (ptp) cc_final: 0.8843 (ppp) REVERT: B 961 LYS cc_start: 0.9434 (ptpp) cc_final: 0.9133 (pttp) REVERT: B 982 ASP cc_start: 0.8476 (p0) cc_final: 0.8215 (p0) REVERT: B 1004 TYR cc_start: 0.9407 (t80) cc_final: 0.9104 (t80) REVERT: B 1099 TRP cc_start: 0.8888 (m100) cc_final: 0.8597 (m100) REVERT: B 1107 TYR cc_start: 0.8307 (t80) cc_final: 0.8056 (t80) REVERT: C 331 ASN cc_start: 0.9207 (t0) cc_final: 0.8947 (p0) REVERT: C 1047 MET cc_start: 0.8944 (tpt) cc_final: 0.8677 (tpt) REVERT: H 81 MET cc_start: 0.4630 (mmt) cc_final: 0.3504 (mmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3898 time to fit residues: 125.6319 Evaluate side-chains 140 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 324 optimal weight: 50.0000 chunk 269 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 26 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 overall best weight: 6.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: