Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 22:36:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/10_2023/6crx_7575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/10_2023/6crx_7575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/10_2023/6crx_7575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/10_2023/6crx_7575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/10_2023/6crx_7575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/10_2023/6crx_7575.pdb" } resolution = 3.9 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= 0.007 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 138 5.16 5 C 16550 2.51 5 N 4197 2.21 5 O 5127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 33 Chain: "B" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8342 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "C" Number of atoms: 8346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8346 Classifications: {'peptide': 1069} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1015} Chain breaks: 6 Chain: "A" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8327 Classifications: {'peptide': 1066} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "D" 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: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" 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: "c" 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: "d" 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: "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: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.05, per 1000 atoms: 0.50 Number of scatterers: 26012 At special positions: 0 Unit cell: (150.38, 146.26, 187.46, 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 138 16.00 O 5127 8.00 N 4197 7.00 C 16550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.00 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.00 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.00 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG B1308 " - " ASN B 589 " " NAG B1309 " - " ASN B 691 " " NAG B1314 " - " ASN B1056 " " NAG B1317 " - " ASN B1116 " " NAG C1307 " - " ASN C 589 " " NAG C1312 " - " ASN C 691 " " NAG D 1 " - " ASN B 602 " " NAG E 1 " - " ASN B 65 " " NAG F 1 " - " ASN B 269 " " NAG G 1 " - " ASN B 783 " " NAG H 1 " - " ASN B1080 " " NAG I 1 " - " ASN B 318 " " NAG J 1 " - " ASN B 699 " " NAG K 1 " - " ASN C 65 " " NAG L 1 " - " ASN C 227 " " NAG M 1 " - " ASN C 318 " " NAG N 1 " - " ASN C 602 " " NAG O 1 " - " ASN C 699 " " NAG P 1 " - " ASN C 783 " " NAG Q 1 " - " ASN C1056 " " NAG R 1 " - " ASN C1080 " " NAG S 1 " - " ASN C1116 " " NAG T 1 " - " ASN C 269 " " NAG U 1 " - " ASN A 269 " " NAG V 1 " - " ASN A 318 " " NAG W 1 " - " ASN A 589 " " NAG X 1 " - " ASN A 602 " " NAG Y 1 " - " ASN A 691 " " NAG Z 1 " - " ASN A 699 " " NAG a 1 " - " ASN A 783 " " NAG b 1 " - " ASN A1056 " " NAG c 1 " - " ASN A1080 " " NAG d 1 " - " ASN A1116 " Time building additional restraints: 10.57 Conformation dependent library (CDL) restraints added in 3.4 seconds 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 49 sheets defined 23.4% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.631A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.606A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.654A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.233A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 491 removed outlier: 3.767A pdb=" N TYR B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.900A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.946A pdb=" N LEU B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.557A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 848 through 864 removed outlier: 3.502A pdb=" N ILE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 872 removed outlier: 3.555A pdb=" N THR B 869 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.757A pdb=" N ILE B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.296A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.797A pdb=" N LEU B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1016 removed outlier: 3.556A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.786A pdb=" N LEU C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.949A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.903A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.695A pdb=" N LEU C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.940A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 746 " --> pdb=" O CYS C 742 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 809 removed outlier: 3.727A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 809 " --> pdb=" O PHE C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.771A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 903 through 923 removed outlier: 3.694A pdb=" N PHE C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 914 " --> pdb=" O ASN C 910 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 923 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.624A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 940 " --> pdb=" O GLN C 936 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 947 " --> pdb=" O THR C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1014 removed outlier: 3.527A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.579A pdb=" N ALA A 339 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.353A pdb=" N ASN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.890A pdb=" N ASP A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.764A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.737A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.980A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 4.044A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.891A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 removed outlier: 4.247A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.557A pdb=" N ARG A 887 " --> pdb=" O GLN A 883 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.505A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.716A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.688A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.556A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 34 removed outlier: 8.731A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 92 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.215A pdb=" N PHE B 47 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.628A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.640A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 14.117A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.710A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.166A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 615 through 616 removed outlier: 4.577A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.449A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.729A pdb=" N LYS B 343 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 383 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 500 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 498 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 497 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 421 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.776A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'B' and resid 640 through 646 removed outlier: 4.938A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 677 " --> pdb=" O CYS B 657 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.283A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 693 through 700 removed outlier: 6.809A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 703 through 709 removed outlier: 3.640A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AB7, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB8, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB9, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 3.603A pdb=" N SER B1105 " --> pdb=" O ALA B1069 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.536A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 52 through 59 removed outlier: 7.516A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.598A pdb=" N ARG C 232 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 157 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 131 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN C 155 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS C 133 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 153 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN C 135 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET C 151 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 137 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS C 149 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 147 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.679A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 12.465A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 157 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 131 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN C 155 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS C 133 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 153 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN C 135 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET C 151 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 137 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS C 149 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 147 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 615 through 616 removed outlier: 4.019A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 312 through 314 removed outlier: 6.591A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE C 551 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 344 through 345 removed outlier: 3.699A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 385 through 390 removed outlier: 3.529A pdb=" N PHE C 387 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AD1, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.245A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 683 through 685 removed outlier: 5.630A pdb=" N ALA C 683 " --> pdb=" O MET A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.725A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.725A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AD6, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AD7, first strand: chain 'C' and resid 821 through 823 removed outlier: 3.537A pdb=" N GLU C 821 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 834 " --> pdb=" O GLU C 821 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 5.164A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.764A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.592A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.571A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 12.612A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'A' and resid 615 through 616 removed outlier: 4.438A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.574A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 421 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A 499 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.557A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AE8, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.140A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 677 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.577A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1029 through 1033 removed outlier: 6.904A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AF3, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AF4, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.782A pdb=" N VAL A1104 " --> pdb=" O PHE A1071 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A1071 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY A1106 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A1065 " --> pdb=" O LYS A1068 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2562 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: 11.11 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8118 1.34 - 1.47: 7104 1.47 - 1.59: 11201 1.59 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 26609 Sorted by residual: bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.470 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C TYR C1070 " pdb=" N PHE C1071 " ideal model delta sigma weight residual 1.331 1.261 0.070 2.07e-02 2.33e+03 1.13e+01 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C ILE A 573 " pdb=" N SER A 574 " ideal model delta sigma weight residual 1.327 1.270 0.057 1.71e-02 3.42e+03 1.11e+01 bond pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sigma weight residual 1.417 1.481 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 26604 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.51: 488 104.51 - 111.94: 12925 111.94 - 119.38: 9012 119.38 - 126.81: 13506 126.81 - 134.24: 273 Bond angle restraints: 36204 Sorted by residual: angle pdb=" C PHE B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C GLN C 908 " pdb=" N PHE C 909 " pdb=" CA PHE C 909 " ideal model delta sigma weight residual 122.06 112.43 9.63 1.86e+00 2.89e-01 2.68e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C ILE A 72 " pdb=" N ASN A 73 " pdb=" CA ASN A 73 " ideal model delta sigma weight residual 120.82 127.95 -7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C THR B 106 " pdb=" N MET B 107 " pdb=" CA MET B 107 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 36199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 14612 17.43 - 34.85: 503 34.85 - 52.28: 107 52.28 - 69.70: 9 69.70 - 87.13: 7 Dihedral angle restraints: 15238 sinusoidal: 5907 harmonic: 9331 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA PHE A 83 " pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta harmonic sigma weight residual -180.00 -133.37 -46.63 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA SER A 35 " pdb=" C SER A 35 " pdb=" N SER A 36 " pdb=" CA SER A 36 " ideal model delta harmonic sigma weight residual -180.00 -134.27 -45.73 0 5.00e+00 4.00e-02 8.36e+01 ... (remaining 15235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4099 0.122 - 0.243: 181 0.243 - 0.365: 19 0.365 - 0.486: 1 0.486 - 0.608: 2 Chirality restraints: 4302 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN A 691 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C1116 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN A 783 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 4299 not shown) Planarity restraints: 4609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C PHE A 83 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A 84 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 968 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 969 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 969 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 969 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 380 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C SER C 380 " 0.055 2.00e-02 2.50e+03 pdb=" O SER C 380 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 381 " -0.019 2.00e-02 2.50e+03 ... (remaining 4606 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3580 2.75 - 3.28: 24044 3.28 - 3.82: 43698 3.82 - 4.36: 50954 4.36 - 4.90: 85587 Nonbonded interactions: 207863 Sorted by model distance: nonbonded pdb=" O GLY B 77 " pdb=" OH TYR B 252 " model vdw 2.208 2.440 nonbonded pdb=" O PHE B1071 " pdb=" OG1 THR B1102 " model vdw 2.224 2.440 nonbonded pdb=" OE1 GLN A 947 " pdb=" OG SER A 985 " model vdw 2.231 2.440 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.249 2.440 ... (remaining 207858 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' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1120 or resid 1308)) selection = (chain 'C' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1120 or resid 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = 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 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'X' 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 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: 1.450 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: 0.020 Extract box with map and model: 8.680 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 67.280 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.010 0.115 26609 Z= 0.650 Angle : 1.118 13.902 36204 Z= 0.592 Chirality : 0.064 0.608 4302 Planarity : 0.007 0.083 4575 Dihedral : 9.421 72.342 9101 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 0.18 % Allowed : 1.12 % Favored : 98.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.73 (0.12), residues: 3161 helix: -3.72 (0.12), residues: 648 sheet: -1.17 (0.20), residues: 606 loop : -2.57 (0.12), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 370 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 375 average time/residue: 0.4137 time to fit residues: 237.1573 Evaluate side-chains 170 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 1.9990 chunk 241 optimal weight: 0.0970 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 0.0970 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 214 ASN B 599 GLN B 641 HIS B 759 ASN B 907 ASN B 993 GLN B1088 GLN C 29 ASN C 122 ASN C 201 GLN C 396 GLN C 445 HIS C 530 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C 993 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 227 ASN A 632 GLN A 661 HIS A 733 ASN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 26609 Z= 0.186 Angle : 0.678 11.809 36204 Z= 0.356 Chirality : 0.046 0.234 4302 Planarity : 0.005 0.065 4575 Dihedral : 6.005 36.213 3437 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.30 % Allowed : 7.05 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 3161 helix: -1.32 (0.17), residues: 669 sheet: -0.75 (0.20), residues: 622 loop : -2.08 (0.13), residues: 1870 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 267 average time/residue: 0.3660 time to fit residues: 159.9450 Evaluate side-chains 177 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2756 time to fit residues: 10.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 50.0000 chunk 286 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 232 optimal weight: 0.0970 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN B 759 ASN B 896 ASN C 118 ASN C 546 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C1005 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 26609 Z= 0.234 Angle : 0.648 8.979 36204 Z= 0.336 Chirality : 0.045 0.224 4302 Planarity : 0.004 0.059 4575 Dihedral : 5.539 31.130 3437 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.08 % Allowed : 9.10 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3161 helix: -0.19 (0.20), residues: 657 sheet: -0.76 (0.20), residues: 620 loop : -1.94 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 201 average time/residue: 0.3323 time to fit residues: 114.4701 Evaluate side-chains 164 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 2.994 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2277 time to fit residues: 11.0321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0067 > 50: distance: 50 - 218: 19.350 distance: 53 - 215: 31.135 distance: 130 - 173: 16.123 distance: 154 - 160: 23.065 distance: 160 - 161: 15.441 distance: 161 - 162: 6.757 distance: 161 - 164: 28.960 distance: 162 - 163: 23.304 distance: 162 - 168: 20.295 distance: 164 - 165: 19.588 distance: 165 - 166: 16.853 distance: 165 - 167: 23.702 distance: 168 - 169: 15.172 distance: 169 - 170: 18.864 distance: 169 - 172: 31.210 distance: 170 - 171: 58.779 distance: 170 - 174: 49.702 distance: 172 - 173: 28.396 distance: 174 - 175: 20.821 distance: 175 - 176: 11.023 distance: 175 - 178: 3.524 distance: 176 - 177: 33.418 distance: 176 - 186: 40.443 distance: 178 - 179: 39.454 distance: 179 - 180: 14.691 distance: 179 - 181: 23.437 distance: 180 - 182: 25.127 distance: 181 - 183: 26.624 distance: 182 - 184: 15.239 distance: 183 - 184: 10.595 distance: 184 - 185: 6.230 distance: 186 - 187: 27.776 distance: 187 - 188: 39.569 distance: 187 - 190: 48.960 distance: 188 - 189: 3.096 distance: 188 - 200: 24.430 distance: 190 - 191: 18.277 distance: 191 - 192: 10.671 distance: 191 - 193: 10.254 distance: 192 - 194: 14.260 distance: 193 - 195: 3.077 distance: 193 - 196: 19.108 distance: 194 - 195: 22.501 distance: 195 - 197: 39.150 distance: 196 - 198: 29.706 distance: 197 - 199: 24.663 distance: 198 - 199: 18.303 distance: 200 - 201: 3.058 distance: 200 - 206: 22.178 distance: 201 - 202: 40.831 distance: 201 - 204: 41.222 distance: 202 - 207: 39.181 distance: 204 - 205: 20.865 distance: 205 - 206: 40.040 distance: 207 - 208: 11.033 distance: 208 - 209: 42.976 distance: 208 - 211: 55.695 distance: 209 - 210: 24.482 distance: 209 - 215: 15.251 distance: 211 - 212: 24.864 distance: 212 - 213: 27.968 distance: 212 - 214: 18.986 distance: 215 - 216: 21.278 distance: 216 - 217: 12.059 distance: 216 - 219: 8.261 distance: 217 - 218: 13.326 distance: 217 - 223: 36.343 distance: 219 - 220: 20.829 distance: 220 - 221: 37.623 distance: 220 - 222: 9.401 distance: 223 - 224: 30.067 distance: 224 - 225: 14.177 distance: 224 - 227: 7.925 distance: 225 - 226: 26.175 distance: 225 - 231: 21.534 distance: 227 - 228: 6.925 distance: 228 - 229: 23.465 distance: 228 - 230: 30.723 distance: 231 - 232: 7.714 distance: 232 - 233: 27.040 distance: 232 - 235: 15.317 distance: 233 - 234: 33.167 distance: 233 - 243: 21.976 distance: 235 - 236: 10.807 distance: 236 - 237: 3.234 distance: 236 - 238: 6.958 distance: 237 - 239: 10.270 distance: 238 - 240: 11.414 distance: 239 - 241: 5.586 distance: 241 - 242: 3.280 distance: 243 - 244: 26.376 distance: 244 - 245: 24.434 distance: 245 - 246: 22.950 distance: 245 - 247: 30.473