Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 03:44:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/05_2023/7xdk_33150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/05_2023/7xdk_33150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/05_2023/7xdk_33150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/05_2023/7xdk_33150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/05_2023/7xdk_33150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/05_2023/7xdk_33150.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.089 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 168 5.16 5 C 24699 2.51 5 N 6477 2.21 5 O 7656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C GLU 644": "OE1" <-> "OE2" Residue "C GLU 1075": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 214": "OE1" <-> "OE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 82": "OD1" <-> "OD2" Residue "O PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39000 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "K" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "O" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} 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 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 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 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 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 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 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 chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "a" 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 chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 20.04, per 1000 atoms: 0.51 Number of scatterers: 39000 At special positions: 0 Unit cell: (183.312, 183.312, 241.2, 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 168 16.00 O 7656 8.00 N 6477 7.00 C 24699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.04 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 508 " distance=2.05 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 573 " distance=2.04 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 141 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 362 " - pdb=" SG CYS B 415 " distance=2.04 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 645 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 141 " - pdb=" SG CYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 362 " - pdb=" SG CYS C 415 " distance=2.04 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 508 " distance=2.04 Simple disulfide: pdb=" SG CYS C 463 " - pdb=" SG CYS C 471 " distance=2.03 Simple disulfide: pdb=" SG CYS C 521 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 600 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 645 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 141 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 195 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1201 " - " ASN A1117 " " NAG A1202 " - " ASN A 692 " " NAG A1203 " - " ASN A1057 " " NAG A1204 " - " ASN A 640 " " NAG B1201 " - " ASN B1117 " " NAG B1202 " - " ASN B 692 " " NAG B1203 " - " ASN B1057 " " NAG B1204 " - " ASN B 640 " " NAG C1201 " - " ASN C1117 " " NAG C1202 " - " ASN C 692 " " NAG C1203 " - " ASN C1057 " " NAG C1204 " - " ASN C 640 " " NAG P 1 " - " ASN A1081 " " NAG Q 1 " - " ASN A 700 " " NAG R 1 " - " ASN A 784 " " NAG S 1 " - " ASN A 314 " " NAG T 1 " - " ASN B1081 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN B 784 " " NAG W 1 " - " ASN B 314 " " NAG X 1 " - " ASN C1081 " " NAG Y 1 " - " ASN C 700 " " NAG Z 1 " - " ASN C 784 " " NAG a 1 " - " ASN C 314 " Time building additional restraints: 16.94 Conformation dependent library (CDL) restraints added in 5.5 seconds 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9270 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 94 sheets defined 16.9% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.607A pdb=" N GLU A 389 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 391 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.619A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.893A pdb=" N ASN A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.252A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 Processing helix chain 'A' and resid 928 through 950 removed outlier: 3.910A pdb=" N GLN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.871A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.857A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.687A pdb=" N GLY F 191 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.668A pdb=" N SER G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.884A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.503A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.597A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.664A pdb=" N TYR B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.534A pdb=" N VAL B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 388 through 393 removed outlier: 4.063A pdb=" N ARG B 391 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.603A pdb=" N SER B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 742 through 766 removed outlier: 4.080A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 747 " --> pdb=" O CYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.706A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 873 " --> pdb=" O THR B 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 869 through 873' Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.039A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 924 Processing helix chain 'B' and resid 928 through 950 removed outlier: 4.090A pdb=" N SER B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 966 removed outlier: 4.097A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1015 Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.823A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'K' and resid 186 through 193 Processing helix chain 'J' and resid 80 through 84 removed outlier: 4.022A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.519A pdb=" N TYR J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.991A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.877A pdb=" N TYR C 143 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 144 " --> pdb=" O GLY C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 144' Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.908A pdb=" N VAL C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.779A pdb=" N LEU C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 removed outlier: 4.668A pdb=" N ARG C 391 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 392 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 720 through 727 Processing helix chain 'C' and resid 729 through 738 removed outlier: 3.776A pdb=" N GLN C 738 " --> pdb=" O ASN C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 766 Processing helix chain 'C' and resid 799 through 809 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.138A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 924 Processing helix chain 'C' and resid 928 through 949 Processing helix chain 'C' and resid 959 through 966 removed outlier: 4.046A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1015 Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.889A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 159 Processing helix chain 'L' and resid 186 through 193 Processing helix chain 'M' and resid 29 through 32 Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.029A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 129 removed outlier: 3.701A pdb=" N GLY M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR N 91 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.624A pdb=" N ALA A 12 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ASN A 46 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR A 252 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 184 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A 211 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 186 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.766A pdb=" N ALA B 558 " --> pdb=" O GLY B 549 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP B 557 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 533 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.951A pdb=" N LYS A 261 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.652A pdb=" N GLY A 92 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY A 88 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.048A pdb=" N VAL A 115 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 302 removed outlier: 6.756A pdb=" N VAL A 578 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN A 300 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 576 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 577 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.740A pdb=" N GLY A 533 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP A 557 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 558 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 548 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 378 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 337 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 345 removed outlier: 6.461A pdb=" N CYS A 344 " --> pdb=" O CYS A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AB5, first strand: chain 'A' and resid 642 through 643 removed outlier: 3.979A pdb=" N TYR A 643 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 684 through 686 Processing sheet with id=AB7, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.549A pdb=" N SER A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A1059 " --> pdb=" O SER A 694 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1053 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.630A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AC1, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 3.535A pdb=" N SER A1106 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.558A pdb=" N TYR F 93 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP F 34 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.606A pdb=" N LYS F 144 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 181 " --> pdb=" O CYS F 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.606A pdb=" N LYS F 144 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR F 177 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.779A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 106 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 13 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.779A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 106 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 13 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 22 removed outlier: 4.031A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.740A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 154 through 155 removed outlier: 3.811A pdb=" N VAL G 151 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS G 195 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS G 208 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 197 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL G 206 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.511A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.870A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 69 through 73 Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.510A pdb=" N ASP E 105 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA E 13 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'E' and resid 45 through 49 removed outlier: 5.699A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 13 through 15 removed outlier: 8.071A pdb=" N ASN B 46 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 252 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 250 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 184 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 211 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE B 186 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.568A pdb=" N ALA C 558 " --> pdb=" O GLY C 549 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP C 557 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 533 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 33 through 40 removed outlier: 3.931A pdb=" N ASP B 270 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.563A pdb=" N GLY B 92 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 115 through 116 removed outlier: 7.217A pdb=" N VAL B 115 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 294 through 302 removed outlier: 5.405A pdb=" N ILE B 295 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR B 582 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN B 297 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 580 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 299 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 577 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.902A pdb=" N ASN B 337 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AE9, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AF1, first strand: chain 'B' and resid 642 through 643 removed outlier: 3.933A pdb=" N TYR B 643 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.647A pdb=" N SER B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B1059 " --> pdb=" O SER B 694 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 704 " --> pdb=" O THR B1049 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 716 through 717 removed outlier: 4.568A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 770 through 772 removed outlier: 5.619A pdb=" N ILE B 771 " --> pdb=" O ASN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.274A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 8 removed outlier: 5.924A pdb=" N GLU K 16 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.310A pdb=" N TRP K 34 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN K 50 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 122 through 124 removed outlier: 5.716A pdb=" N GLY K 140 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL K 183 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU K 142 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER K 181 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS K 144 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU K 179 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 122 through 124 removed outlier: 5.716A pdb=" N GLY K 140 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL K 183 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU K 142 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER K 181 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS K 144 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU K 179 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.378A pdb=" N LYS K 210 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 13 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 13 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR J 98 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.753A pdb=" N ASP J 71 " --> pdb=" O SER J 68 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 117 through 119 removed outlier: 4.164A pdb=" N VAL J 134 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA J 131 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 146 through 151 removed outlier: 3.747A pdb=" N LYS J 146 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 198 " --> pdb=" O LYS J 146 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.621A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.549A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.932A pdb=" N ALA I 13 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.535A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.649A pdb=" N ALA C 12 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ASN C 46 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 252 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE C 184 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 211 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE C 186 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS C 190 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N ALA C 205 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 21 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 35 through 40 removed outlier: 3.579A pdb=" N PHE C 40 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 254 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR C 257 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 273 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 271 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LYS C 261 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 69 through 70 removed outlier: 4.025A pdb=" N GLY C 88 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 101 through 103 removed outlier: 7.123A pdb=" N VAL C 115 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 294 through 302 removed outlier: 6.823A pdb=" N VAL C 578 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN C 300 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 576 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 595 " --> pdb=" O CYS C 632 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS C 632 " --> pdb=" O TYR C 595 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 631 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 337 through 341 removed outlier: 3.711A pdb=" N ASN C 337 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 378 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AI2, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AI3, first strand: chain 'C' and resid 642 through 643 removed outlier: 3.913A pdb=" N TYR C 643 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 674 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 658 " --> pdb=" O SER C 674 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 694 through 710 removed outlier: 6.635A pdb=" N SER C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C1059 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C1053 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AI6, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.387A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 1077 through 1079 Processing sheet with id=AI8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AI9, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.710A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 121 through 124 removed outlier: 3.755A pdb=" N LYS L 144 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR L 177 " --> pdb=" O ASP L 145 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 165 through 166 Processing sheet with id=AJ3, first strand: chain 'L' and resid 199 through 201 Processing sheet with id=AJ4, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.141A pdb=" N LEU M 11 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.141A pdb=" N LEU M 11 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 19 through 22 removed outlier: 3.622A pdb=" N ASP M 71 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 117 through 119 removed outlier: 3.933A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 155 through 156 removed outlier: 4.611A pdb=" N TRP M 149 " --> pdb=" O GLN M 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS M 146 " --> pdb=" O THR M 198 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS M 195 " --> pdb=" O LYS M 208 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS M 208 " --> pdb=" O CYS M 195 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 197 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL M 206 " --> pdb=" O VAL M 197 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS M 199 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER M 204 " --> pdb=" O HIS M 199 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.686A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.798A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.642A pdb=" N THR O 74 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.608A pdb=" N VAL O 11 " --> pdb=" O LYS O 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'O' and resid 45 through 48 removed outlier: 6.011A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE O 48 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) 1390 hydrogen bonds defined for protein. 3690 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: 19.60 Time building geometry restraints manager: 18.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11794 1.33 - 1.46: 10502 1.46 - 1.59: 17373 1.59 - 1.72: 0 1.72 - 1.85: 213 Bond restraints: 39882 Sorted by residual: bond pdb=" CA SER A 332 " pdb=" CB SER A 332 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.61e-02 3.86e+03 1.47e+01 bond pdb=" N VAL B 416 " pdb=" CA VAL B 416 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N VAL B 598 " pdb=" CA VAL B 598 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.02e+01 bond pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N CYS B 415 " pdb=" CA CYS B 415 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.69e+00 ... (remaining 39877 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.96: 971 105.96 - 113.02: 21626 113.02 - 120.08: 13126 120.08 - 127.14: 18129 127.14 - 134.20: 400 Bond angle restraints: 54252 Sorted by residual: angle pdb=" CA VAL B 603 " pdb=" C VAL B 603 " pdb=" N PRO B 604 " ideal model delta sigma weight residual 120.83 124.25 -3.42 6.10e-01 2.69e+00 3.14e+01 angle pdb=" N PHE A 321 " pdb=" CA PHE A 321 " pdb=" C PHE A 321 " ideal model delta sigma weight residual 113.28 107.06 6.22 1.22e+00 6.72e-01 2.60e+01 angle pdb=" CA SER A 332 " pdb=" C SER A 332 " pdb=" O SER A 332 " ideal model delta sigma weight residual 121.87 116.68 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" CA VAL A 333 " pdb=" C VAL A 333 " pdb=" O VAL A 333 " ideal model delta sigma weight residual 120.95 116.51 4.44 1.04e+00 9.25e-01 1.82e+01 angle pdb=" CA VAL B 603 " pdb=" C VAL B 603 " pdb=" O VAL B 603 " ideal model delta sigma weight residual 118.69 115.89 2.80 6.70e-01 2.23e+00 1.75e+01 ... (remaining 54247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 21397 17.97 - 35.94: 1694 35.94 - 53.92: 300 53.92 - 71.89: 67 71.89 - 89.86: 35 Dihedral angle restraints: 23493 sinusoidal: 9045 harmonic: 14448 Sorted by residual: dihedral pdb=" CB CYS C 600 " pdb=" SG CYS C 600 " pdb=" SG CYS C 632 " pdb=" CB CYS C 632 " ideal model delta sinusoidal sigma weight residual -86.00 -165.30 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS A 463 " pdb=" SG CYS A 463 " pdb=" SG CYS A 471 " pdb=" CB CYS A 471 " ideal model delta sinusoidal sigma weight residual 93.00 163.93 -70.93 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS C 319 " pdb=" SG CYS C 319 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -152.15 66.15 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 23490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 6210 0.154 - 0.308: 14 0.308 - 0.462: 1 0.462 - 0.616: 0 0.616 - 0.769: 3 Chirality restraints: 6228 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A1081 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C1081 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1081 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 6225 not shown) Planarity restraints: 6987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 13 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO D 14 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 7 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO I 8 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 8 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 8 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 80 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO G 81 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.024 5.00e-02 4.00e+02 ... (remaining 6984 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2953 2.74 - 3.28: 37477 3.28 - 3.82: 62035 3.82 - 4.36: 73561 4.36 - 4.90: 131626 Nonbonded interactions: 307652 Sorted by model distance: nonbonded pdb=" OD1 ASP O 82 " pdb=" OH TYR O 86 " model vdw 2.200 2.440 nonbonded pdb=" OE1 GLN B 476 " pdb=" OG SER J 30 " model vdw 2.202 2.440 nonbonded pdb=" O GLY E 28 " pdb=" ND2 ASN E 92 " model vdw 2.206 2.520 nonbonded pdb=" OD2 ASP B 513 " pdb=" NE2 GLN B 563 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR F 152 " pdb=" OD1 ASN F 200 " model vdw 2.223 2.440 ... (remaining 307647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.030 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 102.380 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.450 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.062 39882 Z= 0.233 Angle : 0.572 7.763 54252 Z= 0.308 Chirality : 0.047 0.769 6228 Planarity : 0.004 0.048 6963 Dihedral : 13.565 89.861 14052 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer Outliers : 0.12 % 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: -0.52 (0.12), residues: 4923 helix: 2.09 (0.21), residues: 687 sheet: -0.32 (0.13), residues: 1539 loop : -1.01 (0.12), residues: 2697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 463 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 466 average time/residue: 0.5442 time to fit residues: 409.4656 Evaluate side-chains 382 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 380 time to evaluate : 4.597 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3564 time to fit residues: 7.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 385 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 446 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 734 ASN K 6 GLN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 589 ASN C 884 GLN C 890 ASN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C1084 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.086 39882 Z= 0.543 Angle : 0.706 15.913 54252 Z= 0.363 Chirality : 0.051 0.575 6228 Planarity : 0.005 0.053 6963 Dihedral : 4.547 21.564 5346 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.09 % 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: -0.82 (0.12), residues: 4923 helix: 1.64 (0.20), residues: 691 sheet: -0.45 (0.13), residues: 1646 loop : -1.20 (0.12), residues: 2586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 415 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 435 average time/residue: 0.5814 time to fit residues: 405.9411 Evaluate side-chains 417 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 382 time to evaluate : 4.833 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3983 time to fit residues: 32.2831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 447 optimal weight: 2.9990 chunk 483 optimal weight: 20.0000 chunk 398 optimal weight: 3.9990 chunk 443 optimal weight: 0.5980 chunk 152 optimal weight: 8.9990 chunk 359 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: