Starting phenix.real_space_refine on Mon Jul 6 08:44:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw0_39618/07_2026/8yw0_39618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw0_39618/07_2026/8yw0_39618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw0_39618/07_2026/8yw0_39618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw0_39618/07_2026/8yw0_39618.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw0_39618/07_2026/8yw0_39618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw0_39618/07_2026/8yw0_39618.cif" } resolution = 3.55 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 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= 0.002 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 286 5.16 5 C 21544 2.51 5 N 5884 2.21 5 O 6547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34264 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "F" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "G" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "H" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "I" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "J" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 386} Chain: "K" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "M" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "N" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "P" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "Q" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 292 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "R" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 292 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 292 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 7.30, per 1000 atoms: 0.21 Number of scatterers: 34264 At special positions: 0 Unit cell: (217.3, 173.84, 218.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 286 16.00 O 6547 8.00 N 5884 7.00 C 21544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=65, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 18 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.02 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.04 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 125 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 105 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 203 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.04 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.04 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 225 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 18 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 27 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS M 18 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 27 " distance=2.03 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 9 " - pdb=" SG CYS N 18 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 26 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 193 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 200 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 218 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 229 " distance=2.03 Simple disulfide: pdb=" SG CYS T 193 " - pdb=" SG CYS T 205 " distance=2.03 Simple disulfide: pdb=" SG CYS T 200 " - pdb=" SG CYS T 218 " distance=2.03 Simple disulfide: pdb=" SG CYS T 212 " - pdb=" SG CYS T 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG S 1 " - " ASN A 141 " " NAG U 1 " - " ASN B 262 " " NAG V 1 " - " ASN B 200 " " NAG W 1 " - " ASN F 141 " " NAG X 1 " - " ASN H 141 " " NAG Y 1 " - " ASN I 262 " " NAG Z 1 " - " ASN I 200 " " NAG a 1 " - " ASN J 262 " " NAG b 1 " - " ASN J 200 " " NAG c 1 " - " ASN K 262 " " NAG d 1 " - " ASN K 200 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8172 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 94 sheets defined 15.6% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.552A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.221A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 404 through 438 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.543A pdb=" N ALA B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 12 " --> pdb=" O TYR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.569A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 397 Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.883A pdb=" N THR B 402 " --> pdb=" O TYR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.588A pdb=" N ILE B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.526A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.679A pdb=" N MET D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.836A pdb=" N TYR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 4.091A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 404 through 438 removed outlier: 3.583A pdb=" N ARG F 438 " --> pdb=" O ILE F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.600A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.205A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.658A pdb=" N ALA G 286 " --> pdb=" O PRO G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 438 Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.599A pdb=" N TYR H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.989A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS H 259 " --> pdb=" O PRO H 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 255 through 259' Processing helix chain 'H' and resid 404 through 438 Processing helix chain 'I' and resid 350 through 361 removed outlier: 3.724A pdb=" N VAL I 355 " --> pdb=" O PRO I 351 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN I 356 " --> pdb=" O HIS I 352 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 397 Processing helix chain 'I' and resid 398 through 401 removed outlier: 3.980A pdb=" N LEU I 401 " --> pdb=" O PRO I 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 398 through 401' Processing helix chain 'I' and resid 407 through 414 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.799A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.779A pdb=" N VAL J 355 " --> pdb=" O PRO J 351 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 397 Processing helix chain 'J' and resid 398 through 402 removed outlier: 3.870A pdb=" N THR J 402 " --> pdb=" O TYR J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 414 removed outlier: 3.715A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 removed outlier: 3.512A pdb=" N ALA K 11 " --> pdb=" O VAL K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 361 removed outlier: 3.875A pdb=" N VAL K 355 " --> pdb=" O PRO K 351 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN K 356 " --> pdb=" O HIS K 352 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU K 361 " --> pdb=" O TYR K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 397 Processing helix chain 'K' and resid 398 through 402 removed outlier: 3.567A pdb=" N LEU K 401 " --> pdb=" O PRO K 398 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR K 402 " --> pdb=" O TYR K 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 398 through 402' Processing helix chain 'K' and resid 407 through 414 Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 31 through 41 removed outlier: 3.516A pdb=" N GLU L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP L 41 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.680A pdb=" N LEU L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.668A pdb=" N ASN M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 56 removed outlier: 3.540A pdb=" N LEU M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 31 through 41 removed outlier: 3.805A pdb=" N ASP N 41 " --> pdb=" O ARG N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 56 removed outlier: 3.561A pdb=" N LEU N 56 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 152 through 157 removed outlier: 3.981A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.626A pdb=" N SER O 179 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA O 181 " --> pdb=" O ARG O 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 119 Processing helix chain 'P' and resid 152 through 157 removed outlier: 4.067A pdb=" N LYS P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 5.169A pdb=" N SER P 179 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA P 181 " --> pdb=" O ARG P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 119 Processing helix chain 'Q' and resid 152 through 157 removed outlier: 3.541A pdb=" N LYS Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 181 removed outlier: 4.904A pdb=" N SER Q 179 " --> pdb=" O HIS Q 176 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA Q 181 " --> pdb=" O ARG Q 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'R' and resid 209 through 211 No H-bonds generated for 'chain 'R' and resid 209 through 211' Processing helix chain 'R' and resid 225 through 230 Processing helix chain 'T' and resid 209 through 211 No H-bonds generated for 'chain 'T' and resid 209 through 211' Processing helix chain 'T' and resid 225 through 230 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.516A pdb=" N THR A 159 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.397A pdb=" N MET A 31 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 126 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN A 43 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU A 45 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 47 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 120 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.397A pdb=" N MET A 31 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 126 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN A 43 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU A 45 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 47 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 120 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.541A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.522A pdb=" N GLN A 260 " --> pdb=" O MET A 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 306 removed outlier: 5.578A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.810A pdb=" N ALA B 17 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.238A pdb=" N LYS B 66 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 55 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN B 53 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 70 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N SER B 51 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE B 48 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N LYS B 104 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N PHE B 50 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.638A pdb=" N LEU B 102 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ALA B 52 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE B 100 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE B 56 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N THR B 96 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.152A pdb=" N GLU B 109 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 129 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB7, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.500A pdb=" N VAL B 227 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 209 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.526A pdb=" N SER B 182 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 277 Processing sheet with id=AC1, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.679A pdb=" N VAL D 149 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE D 121 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR D 132 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 123 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 256 through 258 removed outlier: 3.718A pdb=" N THR D 244 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE D 207 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 223 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.590A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.507A pdb=" N THR F 159 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 15 through 19 removed outlier: 5.292A pdb=" N MET F 31 " --> pdb=" O MET F 136 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET F 136 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR F 41 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N THR F 126 " --> pdb=" O THR F 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 46 through 48 removed outlier: 3.928A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC8, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD1, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD2, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.503A pdb=" N GLN F 260 " --> pdb=" O MET F 269 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 296 through 306 removed outlier: 5.552A pdb=" N ASP F 298 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS F 321 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 326 through 328 Processing sheet with id=AD5, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AD6, first strand: chain 'F' and resid 387 through 388 removed outlier: 3.514A pdb=" N HIS I 306 " --> pdb=" O TYR I 296 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD8, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.411A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.765A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN G 260 " --> pdb=" O MET G 269 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.591A pdb=" N TYR G 59 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AE4, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AE5, first strand: chain 'G' and resid 297 through 306 removed outlier: 5.591A pdb=" N ASP G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS G 321 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 326 through 329 Processing sheet with id=AE7, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AE8, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.508A pdb=" N TYR J 296 " --> pdb=" O HIS J 306 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AF1, first strand: chain 'H' and resid 15 through 19 removed outlier: 5.277A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 35 " --> pdb=" O LYS H 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 15 through 19 removed outlier: 5.277A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 35 " --> pdb=" O LYS H 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR H 59 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AF5, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AF6, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'H' and resid 260 through 262 Processing sheet with id=AF8, first strand: chain 'H' and resid 296 through 306 removed outlier: 5.494A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 326 through 328 removed outlier: 3.680A pdb=" N ALA H 344 " --> pdb=" O CYS H 328 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AG2, first strand: chain 'H' and resid 387 through 388 removed outlier: 3.515A pdb=" N HIS K 306 " --> pdb=" O TYR K 296 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 17 through 18 removed outlier: 3.537A pdb=" N ALA I 17 " --> pdb=" O SER I 30 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 46 through 54 removed outlier: 6.357A pdb=" N HIS I 99 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ALA I 52 " --> pdb=" O MET I 97 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N MET I 97 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ILE I 54 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N GLY I 95 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 66 through 70 Processing sheet with id=AG6, first strand: chain 'I' and resid 84 through 86 removed outlier: 4.236A pdb=" N GLU I 109 " --> pdb=" O TYR I 129 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 149 through 156 removed outlier: 3.595A pdb=" N VAL I 267 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.747A pdb=" N VAL I 227 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY I 209 " --> pdb=" O TYR I 199 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AH1, first strand: chain 'I' and resid 274 through 277 Processing sheet with id=AH2, first strand: chain 'J' and resid 17 through 19 removed outlier: 3.515A pdb=" N ALA J 17 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS J 19 " --> pdb=" O CYS J 28 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS J 28 " --> pdb=" O CYS J 19 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 75 through 79 removed outlier: 4.946A pdb=" N GLY J 55 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR J 65 " --> pdb=" O GLN J 53 " (cutoff:3.500A) removed outlier: 12.442A pdb=" N GLN J 53 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE J 67 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 11.793A pdb=" N SER J 51 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 13.164A pdb=" N TYR J 69 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 16.669A pdb=" N GLN J 49 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA J 103 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 15.472A pdb=" N ILE J 56 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 18.617A pdb=" N VAL J 93 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 84 through 86 removed outlier: 4.229A pdb=" N GLU J 109 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AH6, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AH7, first strand: chain 'J' and resid 167 through 169 Processing sheet with id=AH8, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH9, first strand: chain 'J' and resid 181 through 183 Processing sheet with id=AI1, first strand: chain 'J' and resid 274 through 277 Processing sheet with id=AI2, first strand: chain 'K' and resid 17 through 18 Processing sheet with id=AI3, first strand: chain 'K' and resid 46 through 54 removed outlier: 11.310A pdb=" N PHE K 50 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 11.771A pdb=" N LEU K 102 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ALA K 52 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE K 100 " --> pdb=" O ALA K 52 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 66 through 69 Processing sheet with id=AI5, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.200A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 148 through 152 removed outlier: 3.611A pdb=" N VAL K 267 " --> pdb=" O LYS K 149 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AI8, first strand: chain 'K' and resid 175 through 176 Processing sheet with id=AI9, first strand: chain 'K' and resid 197 through 199 removed outlier: 3.571A pdb=" N GLY K 209 " --> pdb=" O TYR K 199 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 274 through 277 Processing sheet with id=AJ2, first strand: chain 'O' and resid 149 through 150 removed outlier: 6.367A pdb=" N PHE O 121 " --> pdb=" O TYR O 132 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR O 132 " --> pdb=" O PHE O 121 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL O 123 " --> pdb=" O THR O 130 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 256 through 259 removed outlier: 4.672A pdb=" N PHE O 207 " --> pdb=" O LEU O 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY O 191 " --> pdb=" O TYR O 202 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE O 223 " --> pdb=" O VAL O 231 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 256 through 259 removed outlier: 6.345A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA O 232 " --> pdb=" O TRP O 251 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'P' and resid 149 through 150 removed outlier: 6.397A pdb=" N PHE P 121 " --> pdb=" O TYR P 132 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR P 132 " --> pdb=" O PHE P 121 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL P 123 " --> pdb=" O THR P 130 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'P' and resid 256 through 259 removed outlier: 5.000A pdb=" N PHE P 207 " --> pdb=" O LEU P 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY P 191 " --> pdb=" O TYR P 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA P 232 " --> pdb=" O ILE P 223 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'P' and resid 256 through 259 removed outlier: 6.118A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.593A pdb=" N VAL Q 149 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE Q 121 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR Q 132 " --> pdb=" O PHE Q 121 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL Q 123 " --> pdb=" O THR Q 130 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR Q 132 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER Q 163 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS Q 170 " --> pdb=" O LYS Q 161 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Q' and resid 256 through 259 removed outlier: 3.565A pdb=" N THR Q 257 " --> pdb=" O THR Q 250 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR Q 244 " --> pdb=" O ILE Q 209 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE Q 207 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY Q 191 " --> pdb=" O TYR Q 202 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE Q 223 " --> pdb=" O VAL Q 231 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Q' and resid 256 through 259 removed outlier: 3.565A pdb=" N THR Q 257 " --> pdb=" O THR Q 250 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL Q 249 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL Q 234 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TRP Q 251 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA Q 232 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 197 through 199 Processing sheet with id=AK3, first strand: chain 'R' and resid 197 through 199 Processing sheet with id=AK4, first strand: chain 'T' and resid 197 through 199 1217 hydrogen bonds defined for protein. 3195 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: 8.07 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11142 1.35 - 1.47: 8655 1.47 - 1.59: 14963 1.59 - 1.72: 2 1.72 - 1.84: 382 Bond restraints: 35144 Sorted by residual: bond pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.81e+00 bond pdb=" CB PRO J 363 " pdb=" CG PRO J 363 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.20e+00 bond pdb=" CB PRO A 22 " pdb=" CG PRO A 22 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.55e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 BMA W 3 " pdb=" C2 BMA W 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 35139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 47040 2.13 - 4.27: 698 4.27 - 6.40: 104 6.40 - 8.54: 14 8.54 - 10.67: 4 Bond angle restraints: 47860 Sorted by residual: angle pdb=" CA PRO B 363 " pdb=" N PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 112.00 103.49 8.51 1.40e+00 5.10e-01 3.69e+01 angle pdb=" N ILE J 217 " pdb=" CA ILE J 217 " pdb=" C ILE J 217 " ideal model delta sigma weight residual 112.96 107.10 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" CA PRO Q 143 " pdb=" N PRO Q 143 " pdb=" CD PRO Q 143 " ideal model delta sigma weight residual 112.00 104.46 7.54 1.40e+00 5.10e-01 2.90e+01 angle pdb=" CA PRO J 363 " pdb=" N PRO J 363 " pdb=" CD PRO J 363 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" CA PRO K 398 " pdb=" N PRO K 398 " pdb=" CD PRO K 398 " ideal model delta sigma weight residual 112.00 105.10 6.90 1.40e+00 5.10e-01 2.43e+01 ... (remaining 47855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 20191 22.08 - 44.17: 1155 44.17 - 66.25: 110 66.25 - 88.33: 85 88.33 - 110.41: 46 Dihedral angle restraints: 21587 sinusoidal: 8850 harmonic: 12737 Sorted by residual: dihedral pdb=" CA GLU K 247 " pdb=" C GLU K 247 " pdb=" N PRO K 248 " pdb=" CA PRO K 248 " ideal model delta harmonic sigma weight residual 180.00 137.76 42.24 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CB CYS I 203 " pdb=" SG CYS I 203 " pdb=" SG CYS I 220 " pdb=" CB CYS I 220 " ideal model delta sinusoidal sigma weight residual -86.00 -20.90 -65.10 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS J 19 " pdb=" SG CYS J 19 " pdb=" SG CYS J 125 " pdb=" CB CYS J 125 " ideal model delta sinusoidal sigma weight residual 93.00 154.96 -61.96 1 1.00e+01 1.00e-02 5.09e+01 ... (remaining 21584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4794 0.073 - 0.146: 588 0.146 - 0.219: 19 0.219 - 0.292: 11 0.292 - 0.365: 1 Chirality restraints: 5413 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN J 262 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 5410 not shown) Planarity restraints: 6166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 397 " -0.087 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO K 398 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO K 398 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO K 398 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 142 " 0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO Q 143 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO Q 143 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO Q 143 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 362 " 0.069 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO B 363 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 363 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 363 " 0.054 5.00e-02 4.00e+02 ... (remaining 6163 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 298 2.63 - 3.20: 29075 3.20 - 3.76: 46951 3.76 - 4.33: 63630 4.33 - 4.90: 110100 Nonbonded interactions: 250054 Sorted by model distance: nonbonded pdb=" OG SER R 201 " pdb=" OD2 ASP R 220 " model vdw 2.059 3.040 nonbonded pdb=" OG SER E 201 " pdb=" OD2 ASP E 220 " model vdw 2.085 3.040 nonbonded pdb=" OG SER T 201 " pdb=" OD2 ASP T 220 " model vdw 2.126 3.040 nonbonded pdb=" OE1 GLU I 166 " pdb=" OH TYR L 49 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR H 300 " pdb=" OG1 THR H 319 " model vdw 2.190 3.040 ... (remaining 250049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 2.400 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.300 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4585 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 : 0.003 0.121 35242 Z= 0.155 Angle : 0.650 10.669 48089 Z= 0.340 Chirality : 0.046 0.365 5413 Planarity : 0.006 0.129 6155 Dihedral : 15.024 110.413 13220 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.20 % Favored : 93.58 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 4358 helix: 2.17 (0.23), residues: 575 sheet: -0.43 (0.16), residues: 1092 loop : -1.39 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 115 TYR 0.027 0.001 TYR F 93 PHE 0.027 0.001 PHE K 50 TRP 0.014 0.001 TRP P 195 HIS 0.016 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (35144) covalent geometry : angle 0.64107 / 0.34 (47860) SS BOND : bond 0.00420 / 0.29 ( 65) SS BOND : angle 1.49954 / 1.04 ( 130) hydrogen bonds : bond 0.23712 / 15.92 ( 1151) hydrogen bonds : angle 7.93909 / 5.55 ( 3195) link_BETA1-4 : bond 0.00785 / 0.51 ( 22) link_BETA1-4 : angle 2.06708 / 1.32 ( 66) link_NAG-ASN : bond 0.00356 / 0.16 ( 11) link_NAG-ASN : angle 1.68598 / 1.00 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 846 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.5404 (m110) cc_final: 0.5135 (m110) REVERT: D 142 LYS cc_start: 0.6563 (ptmm) cc_final: 0.5917 (ptmm) REVERT: D 177 MET cc_start: 0.6995 (mtm) cc_final: 0.6349 (mtp) REVERT: H 370 CYS cc_start: 0.3706 (m) cc_final: 0.3428 (m) REVERT: I 50 PHE cc_start: 0.5838 (m-80) cc_final: 0.5563 (m-80) REVERT: K 286 LEU cc_start: 0.4393 (mt) cc_final: 0.3572 (mp) REVERT: O 221 ARG cc_start: 0.6207 (tpp-160) cc_final: 0.5405 (ttm-80) REVERT: O 240 GLU cc_start: 0.6492 (tm-30) cc_final: 0.5914 (pm20) REVERT: P 139 LYS cc_start: 0.6050 (mttm) cc_final: 0.5839 (mtmt) REVERT: P 161 LYS cc_start: 0.6584 (ttmm) cc_final: 0.5745 (tttt) REVERT: Q 193 TYR cc_start: 0.6368 (m-80) cc_final: 0.6082 (m-80) outliers start: 1 outliers final: 0 residues processed: 847 average time/residue: 0.2102 time to fit residues: 289.6112 Evaluate side-chains 587 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 30.0000 chunk 155 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 32 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 235 GLN H 30 GLN J 120 ASN J 131 HIS ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 GLN K 306 HIS K 340 GLN O 197 HIS P 176 HIS Q 201 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133612 restraints weight = 47343.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138132 restraints weight = 23093.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139213 restraints weight = 14202.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140588 restraints weight = 12147.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141067 restraints weight = 9706.951| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5314 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 35242 Z= 0.142 Angle : 0.683 12.272 48089 Z= 0.342 Chirality : 0.046 0.276 5413 Planarity : 0.005 0.075 6155 Dihedral : 9.261 71.486 5420 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Rotamer: Outliers : 2.31 % Allowed : 10.01 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 4358 helix: 2.09 (0.22), residues: 575 sheet: -0.46 (0.14), residues: 1376 loop : -1.29 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 373 TYR 0.026 0.002 TYR A 85 PHE 0.019 0.002 PHE P 207 TRP 0.021 0.002 TRP K 235 HIS 0.011 0.001 HIS D 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (35144) covalent geometry : angle 0.67360 / 0.34 (47860) SS BOND : bond 0.00341 / 0.26 ( 65) SS BOND : angle 1.15937 / 0.89 ( 130) hydrogen bonds : bond 0.03803 / 2.49 ( 1151) hydrogen bonds : angle 5.57183 / 3.92 ( 3195) link_BETA1-4 : bond 0.00725 / 0.48 ( 22) link_BETA1-4 : angle 2.66372 / 1.70 ( 66) link_NAG-ASN : bond 0.00409 / 0.20 ( 11) link_NAG-ASN : angle 1.45964 / 0.87 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 641 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.5856 (t70) cc_final: 0.4622 (t0) REVERT: A 384 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7652 (mmtm) REVERT: D 141 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7032 (mtt) REVERT: F 88 MET cc_start: 0.6188 (mmm) cc_final: 0.5899 (mmm) REVERT: I 50 PHE cc_start: 0.5861 (m-80) cc_final: 0.5540 (m-80) REVERT: I 169 MET cc_start: 0.5597 (mmm) cc_final: 0.5143 (mmm) REVERT: J 373 MET cc_start: 0.5354 (mmt) cc_final: 0.5064 (mmt) REVERT: K 169 MET cc_start: 0.7235 (mmt) cc_final: 0.6966 (mmm) REVERT: K 358 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.6268 (t80) REVERT: M 48 TYR cc_start: 0.4299 (t80) cc_final: 0.3946 (t80) REVERT: M 52 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5822 (mt) REVERT: N 35 THR cc_start: 0.7332 (m) cc_final: 0.6922 (p) REVERT: O 221 ARG cc_start: 0.6416 (tpp-160) cc_final: 0.6115 (ttm110) REVERT: O 240 GLU cc_start: 0.6120 (tm-30) cc_final: 0.5627 (pm20) REVERT: P 128 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6786 (mmmm) REVERT: P 139 LYS cc_start: 0.5885 (mttm) cc_final: 0.5456 (mtmt) REVERT: P 161 LYS cc_start: 0.7123 (ttmm) cc_final: 0.6354 (ttpt) REVERT: P 202 TYR cc_start: 0.7536 (t80) cc_final: 0.7227 (t80) REVERT: P 224 PHE cc_start: 0.4852 (m-80) cc_final: 0.4577 (m-80) outliers start: 86 outliers final: 44 residues processed: 679 average time/residue: 0.2002 time to fit residues: 227.0608 Evaluate side-chains 590 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 543 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 301 CYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 251 LYS Chi-restraints excluded: chain K residue 358 TYR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 176 HIS Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 107 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 363 optimal weight: 40.0000 chunk 217 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN B 255 HIS D 186 HIS ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS G 235 GLN H 18 HIS H 270 ASN I 53 GLN I 77 ASN I 340 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 HIS J 77 ASN J 218 ASN K 53 GLN K 348 HIS O 197 HIS P 176 HIS P 196 HIS ** Q 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 196 HIS E 199 GLN T 199 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.188396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147757 restraints weight = 47908.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148984 restraints weight = 25451.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150060 restraints weight = 16596.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150831 restraints weight = 14863.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150840 restraints weight = 12569.414| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 35242 Z= 0.234 Angle : 0.853 17.994 48089 Z= 0.431 Chirality : 0.051 0.380 5413 Planarity : 0.006 0.082 6155 Dihedral : 6.816 59.961 5420 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.45 % Favored : 93.32 % Rotamer: Outliers : 4.02 % Allowed : 13.20 % Favored : 82.78 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4358 helix: 1.97 (0.22), residues: 551 sheet: -0.53 (0.14), residues: 1308 loop : -1.36 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 266 TYR 0.035 0.002 TYR G 242 PHE 0.041 0.003 PHE I 92 TRP 0.029 0.003 TRP A 89 HIS 0.064 0.002 HIS P 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (35144) covalent geometry : angle 0.83182 / 0.43 (47860) SS BOND : bond 0.00370 / 0.23 ( 65) SS BOND : angle 1.41813 / 1.07 ( 130) hydrogen bonds : bond 0.04574 / 2.99 ( 1151) hydrogen bonds : angle 5.40083 / 3.82 ( 3195) link_BETA1-4 : bond 0.00859 / 0.49 ( 22) link_BETA1-4 : angle 3.71776 / 2.36 ( 66) link_NAG-ASN : bond 0.00474 / 0.28 ( 11) link_NAG-ASN : angle 4.61815 / 2.21 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 738 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.7178 (tpp80) cc_final: 0.6892 (mmm-85) REVERT: D 162 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8162 (mtpp) REVERT: F 87 PHE cc_start: 0.8334 (m-10) cc_final: 0.8082 (m-10) REVERT: F 122 TYR cc_start: 0.8169 (m-80) cc_final: 0.7819 (m-80) REVERT: F 301 CYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6217 (m) REVERT: F 302 THR cc_start: 0.6286 (OUTLIER) cc_final: 0.5989 (p) REVERT: G 2 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7529 (mm-30) REVERT: G 393 SER cc_start: 0.7857 (m) cc_final: 0.7083 (t) REVERT: H 209 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6963 (mm-30) REVERT: I 76 GLU cc_start: 0.6288 (mp0) cc_final: 0.5720 (mp0) REVERT: I 169 MET cc_start: 0.7033 (mmm) cc_final: 0.6281 (mmm) REVERT: I 307 GLU cc_start: 0.8320 (pm20) cc_final: 0.7679 (pt0) REVERT: J 45 MET cc_start: 0.7756 (mmt) cc_final: 0.7088 (mmm) REVERT: J 132 ASP cc_start: 0.7659 (t0) cc_final: 0.7050 (p0) REVERT: K 71 ASP cc_start: 0.7078 (t0) cc_final: 0.6283 (t0) REVERT: K 130 HIS cc_start: 0.6480 (p-80) cc_final: 0.6172 (t-90) REVERT: K 169 MET cc_start: 0.7876 (mmt) cc_final: 0.7596 (mmm) REVERT: K 299 LEU cc_start: 0.9047 (pp) cc_final: 0.8686 (pp) REVERT: K 325 MET cc_start: 0.7533 (ppp) cc_final: 0.7083 (ptt) REVERT: P 161 LYS cc_start: 0.7079 (ttmm) cc_final: 0.5909 (tttt) REVERT: P 180 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6924 (t0) REVERT: Q 111 MET cc_start: 0.8097 (pmm) cc_final: 0.7800 (pmm) REVERT: E 200 CYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3871 (p) outliers start: 150 outliers final: 68 residues processed: 826 average time/residue: 0.1972 time to fit residues: 271.8808 Evaluate side-chains 635 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 563 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 301 CYS Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 342 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 255 MET Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain Q residue 259 VAL Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 271 optimal weight: 3.9990 chunk 412 optimal weight: 0.0870 chunk 312 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 GLN B 170 HIS B 187 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS F 118 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN G 355 HIS H 260 GLN H 270 ASN H 325 ASN I 26 HIS I 53 GLN I 99 HIS I 328 HIS J 77 ASN J 94 HIS J 120 ASN J 218 ASN J 352 HIS K 170 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS Q 192 HIS Q 197 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.185211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142251 restraints weight = 46987.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144008 restraints weight = 22797.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144697 restraints weight = 15580.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145440 restraints weight = 14119.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145573 restraints weight = 12154.244| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.7743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35242 Z= 0.148 Angle : 0.674 13.172 48089 Z= 0.336 Chirality : 0.046 0.403 5413 Planarity : 0.005 0.093 6155 Dihedral : 6.008 58.423 5420 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 3.25 % Allowed : 16.98 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 4358 helix: 2.23 (0.22), residues: 551 sheet: -0.34 (0.14), residues: 1280 loop : -1.30 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 68 TYR 0.021 0.002 TYR A 76 PHE 0.022 0.001 PHE G 189 TRP 0.025 0.001 TRP B 235 HIS 0.014 0.001 HIS J 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (35144) covalent geometry : angle 0.66307 / 0.33 (47860) SS BOND : bond 0.00350 / 0.20 ( 65) SS BOND : angle 1.22965 / 0.88 ( 130) hydrogen bonds : bond 0.03345 / 2.18 ( 1151) hydrogen bonds : angle 4.89550 / 3.47 ( 3195) link_BETA1-4 : bond 0.00902 / 0.49 ( 22) link_BETA1-4 : angle 2.41102 / 1.53 ( 66) link_NAG-ASN : bond 0.01013 / 0.51 ( 11) link_NAG-ASN : angle 2.44974 / 1.72 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 611 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8615 (m-80) cc_final: 0.8404 (m-80) REVERT: A 320 TYR cc_start: 0.8246 (p90) cc_final: 0.8044 (p90) REVERT: B 299 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7362 (pp) REVERT: F 245 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7419 (mmtt) REVERT: G 99 GLU cc_start: 0.6873 (mp0) cc_final: 0.6235 (tm-30) REVERT: G 269 MET cc_start: 0.7574 (mmm) cc_final: 0.7243 (mmm) REVERT: G 393 SER cc_start: 0.8266 (m) cc_final: 0.7481 (t) REVERT: H 209 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6890 (mm-30) REVERT: H 386 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6985 (t-90) REVERT: I 71 ASP cc_start: 0.7522 (p0) cc_final: 0.7269 (p0) REVERT: I 128 GLN cc_start: 0.7165 (pp30) cc_final: 0.6460 (tt0) REVERT: I 307 GLU cc_start: 0.8246 (pm20) cc_final: 0.7667 (pt0) REVERT: I 373 MET cc_start: 0.7392 (tpp) cc_final: 0.6744 (mtt) REVERT: J 115 ILE cc_start: 0.4020 (tt) cc_final: 0.3758 (tt) REVERT: J 261 ASP cc_start: 0.6265 (t70) cc_final: 0.5898 (t70) REVERT: K 97 MET cc_start: 0.5912 (ppp) cc_final: 0.5645 (tmm) REVERT: K 299 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8689 (pp) REVERT: K 325 MET cc_start: 0.7999 (ppp) cc_final: 0.7227 (ptt) REVERT: M 18 CYS cc_start: 0.5171 (m) cc_final: 0.4723 (m) REVERT: N 36 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5476 (mp) REVERT: P 177 MET cc_start: 0.6463 (mpp) cc_final: 0.5554 (mtp) REVERT: P 180 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6876 (t0) REVERT: Q 139 LYS cc_start: 0.5146 (mtmt) cc_final: 0.3680 (mttp) outliers start: 121 outliers final: 72 residues processed: 685 average time/residue: 0.1874 time to fit residues: 217.0295 Evaluate side-chains 612 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 535 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 386 HIS Chi-restraints excluded: chain H residue 393 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 328 HIS Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 333 ASP Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 328 HIS Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 242 SER Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 173 optimal weight: 0.9980 chunk 371 optimal weight: 7.9990 chunk 430 optimal weight: 50.0000 chunk 260 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 367 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 32 GLN ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS D 201 GLN F 32 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN F 270 ASN F 333 HIS G 142 GLN G 211 ASN H 230 HIS H 264 ASN H 270 ASN I 236 GLN J 120 ASN J 348 HIS J 352 HIS K 226 HIS K 340 GLN M 42 ASN O 196 HIS R 199 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119051 restraints weight = 46956.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120444 restraints weight = 24245.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120347 restraints weight = 17064.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121111 restraints weight = 15782.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121160 restraints weight = 13193.622| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 1.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 35242 Z= 0.261 Angle : 0.828 12.320 48089 Z= 0.427 Chirality : 0.051 0.377 5413 Planarity : 0.006 0.080 6155 Dihedral : 6.521 59.275 5420 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.36 % Rotamer: Outliers : 5.04 % Allowed : 16.85 % Favored : 78.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 4358 helix: 2.09 (0.22), residues: 531 sheet: -0.66 (0.14), residues: 1372 loop : -1.36 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG Q 108 TYR 0.029 0.002 TYR A 93 PHE 0.041 0.003 PHE K 50 TRP 0.024 0.002 TRP B 235 HIS 0.065 0.002 HIS I 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 (35144) covalent geometry : angle 0.81732 / 0.42 (47860) SS BOND : bond 0.00418 / 0.26 ( 65) SS BOND : angle 1.79619 / 1.22 ( 130) hydrogen bonds : bond 0.04626 / 3.00 ( 1151) hydrogen bonds : angle 5.34134 / 3.77 ( 3195) link_BETA1-4 : bond 0.00861 / 0.50 ( 22) link_BETA1-4 : angle 2.27613 / 1.56 ( 66) link_NAG-ASN : bond 0.02174 / 1.13 ( 11) link_NAG-ASN : angle 2.54482 / 1.77 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 542 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8091 (mmm) cc_final: 0.7832 (mmm) REVERT: A 269 MET cc_start: 0.7911 (ttm) cc_final: 0.7662 (tpp) REVERT: B 7 ASN cc_start: 0.7132 (t0) cc_final: 0.6508 (t0) REVERT: B 174 ASP cc_start: 0.8382 (p0) cc_final: 0.7984 (p0) REVERT: B 220 CYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5544 (p) REVERT: B 251 LYS cc_start: 0.8247 (tptp) cc_final: 0.8037 (tptp) REVERT: B 302 ASP cc_start: 0.7814 (p0) cc_final: 0.7499 (p0) REVERT: B 387 MET cc_start: 0.6686 (ttm) cc_final: 0.6288 (ttm) REVERT: F 95 PHE cc_start: 0.6518 (t80) cc_final: 0.6278 (t80) REVERT: F 174 ASP cc_start: 0.8324 (t0) cc_final: 0.7838 (t0) REVERT: F 280 MET cc_start: 0.8422 (ptp) cc_final: 0.8089 (ptp) REVERT: F 384 LYS cc_start: 0.4582 (mptt) cc_final: 0.2299 (mptt) REVERT: G 182 ASP cc_start: 0.7778 (t70) cc_final: 0.7482 (t0) REVERT: G 269 MET cc_start: 0.8616 (mmm) cc_final: 0.8052 (mmm) REVERT: G 397 VAL cc_start: 0.8999 (t) cc_final: 0.8760 (p) REVERT: H 269 MET cc_start: 0.8271 (mmm) cc_final: 0.7808 (mmm) REVERT: H 386 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7955 (t-90) REVERT: H 402 MET cc_start: 0.8520 (tpp) cc_final: 0.8037 (mmt) REVERT: I 169 MET cc_start: 0.7939 (mmm) cc_final: 0.7679 (mmt) REVERT: I 260 LEU cc_start: 0.7486 (pt) cc_final: 0.7251 (pt) REVERT: I 337 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8684 (mt) REVERT: I 373 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6985 (mtt) REVERT: J 10 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7452 (mtmt) REVERT: J 40 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8110 (mt-10) REVERT: J 325 MET cc_start: 0.8863 (ptm) cc_final: 0.8367 (ptt) REVERT: K 50 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: K 57 ASP cc_start: 0.7405 (t0) cc_final: 0.7102 (t0) REVERT: K 84 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (mtmm) REVERT: K 128 GLN cc_start: 0.7370 (pp30) cc_final: 0.6973 (tt0) REVERT: K 132 ASP cc_start: 0.8477 (t0) cc_final: 0.8069 (p0) REVERT: M 18 CYS cc_start: 0.5520 (m) cc_final: 0.5151 (m) REVERT: N 36 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5401 (mp) REVERT: O 251 TRP cc_start: 0.8859 (p90) cc_final: 0.8591 (p90) REVERT: Q 111 MET cc_start: 0.8037 (pmm) cc_final: 0.7520 (pmm) REVERT: Q 139 LYS cc_start: 0.5312 (mtmt) cc_final: 0.4997 (pttp) REVERT: Q 161 LYS cc_start: 0.8450 (mttm) cc_final: 0.8097 (ttmm) REVERT: Q 224 PHE cc_start: 0.8576 (m-80) cc_final: 0.8124 (m-80) REVERT: Q 256 VAL cc_start: 0.6862 (OUTLIER) cc_final: 0.6335 (p) outliers start: 188 outliers final: 100 residues processed: 685 average time/residue: 0.1984 time to fit residues: 226.8194 Evaluate side-chains 555 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 447 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 386 HIS Chi-restraints excluded: chain H residue 393 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 73 HIS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 373 MET Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 132 ASP Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 328 HIS Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 234 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 256 VAL Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 302 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 357 optimal weight: 0.9980 chunk 350 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 61 optimal weight: 0.0370 chunk 241 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 187 GLN B 53 GLN B 236 GLN B 255 HIS F 32 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN J 352 HIS ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN O 197 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.177515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131771 restraints weight = 46171.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132994 restraints weight = 22876.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133560 restraints weight = 16929.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134367 restraints weight = 14831.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135651 restraints weight = 12480.744| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 1.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35242 Z= 0.113 Angle : 0.626 10.593 48089 Z= 0.316 Chirality : 0.045 0.271 5413 Planarity : 0.005 0.057 6155 Dihedral : 5.883 58.467 5420 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.93 % Favored : 94.88 % Rotamer: Outliers : 3.33 % Allowed : 19.34 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4358 helix: 2.39 (0.23), residues: 535 sheet: -0.51 (0.14), residues: 1320 loop : -1.18 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 115 TYR 0.024 0.001 TYR G 233 PHE 0.018 0.001 PHE G 189 TRP 0.016 0.001 TRP B 235 HIS 0.010 0.001 HIS G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (35144) covalent geometry : angle 0.61821 / 0.31 (47860) SS BOND : bond 0.00491 / 0.36 ( 65) SS BOND : angle 1.35461 / 0.94 ( 130) hydrogen bonds : bond 0.03325 / 2.19 ( 1151) hydrogen bonds : angle 4.84832 / 3.44 ( 3195) link_BETA1-4 : bond 0.00612 / 0.38 ( 22) link_BETA1-4 : angle 1.78068 / 1.15 ( 66) link_NAG-ASN : bond 0.00496 / 0.25 ( 11) link_NAG-ASN : angle 2.02194 / 1.39 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 478 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.8403 (p0) cc_final: 0.7963 (p0) REVERT: B 302 ASP cc_start: 0.7705 (p0) cc_final: 0.7457 (p0) REVERT: B 387 MET cc_start: 0.6652 (ttm) cc_final: 0.6233 (ttm) REVERT: F 174 ASP cc_start: 0.8174 (t0) cc_final: 0.7713 (t0) REVERT: F 302 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7450 (p) REVERT: G 182 ASP cc_start: 0.7798 (t70) cc_final: 0.7574 (t70) REVERT: G 280 MET cc_start: 0.9111 (mtm) cc_final: 0.8883 (mtm) REVERT: H 269 MET cc_start: 0.8291 (mmm) cc_final: 0.7936 (mmm) REVERT: H 411 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7755 (mt0) REVERT: H 432 THR cc_start: 0.6298 (t) cc_final: 0.5959 (t) REVERT: I 76 GLU cc_start: 0.7243 (mp0) cc_final: 0.6968 (mp0) REVERT: I 373 MET cc_start: 0.7248 (tpp) cc_final: 0.6962 (mtt) REVERT: J 7 ASN cc_start: 0.7983 (t0) cc_final: 0.7759 (t0) REVERT: J 253 LYS cc_start: 0.9037 (mttt) cc_final: 0.8654 (ptpt) REVERT: J 325 MET cc_start: 0.8605 (ptm) cc_final: 0.8146 (ptt) REVERT: K 57 ASP cc_start: 0.7427 (t0) cc_final: 0.6983 (t0) REVERT: K 128 GLN cc_start: 0.7311 (pp30) cc_final: 0.7074 (tt0) REVERT: K 132 ASP cc_start: 0.8418 (t0) cc_final: 0.7916 (p0) REVERT: K 328 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7273 (t-90) REVERT: K 376 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7475 (tp) REVERT: N 36 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5819 (mp) REVERT: O 165 LYS cc_start: 0.8615 (tttm) cc_final: 0.8382 (tttm) REVERT: O 221 ARG cc_start: 0.8406 (mmt-90) cc_final: 0.8156 (tpp-160) REVERT: Q 111 MET cc_start: 0.8247 (pmm) cc_final: 0.7681 (pmm) REVERT: Q 139 LYS cc_start: 0.5154 (mtmt) cc_final: 0.4817 (pttp) REVERT: Q 161 LYS cc_start: 0.8449 (mttm) cc_final: 0.8109 (ttmm) REVERT: Q 224 PHE cc_start: 0.8534 (m-80) cc_final: 0.7980 (m-80) outliers start: 124 outliers final: 72 residues processed: 568 average time/residue: 0.1847 time to fit residues: 176.9663 Evaluate side-chains 507 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 431 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 215 MET Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 328 HIS Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 141 MET Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 157 optimal weight: 4.9990 chunk 268 optimal weight: 7.9990 chunk 380 optimal weight: 2.9990 chunk 396 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 chunk 421 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 GLN ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 HIS J 352 HIS ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN O 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117542 restraints weight = 46108.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117311 restraints weight = 27054.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117802 restraints weight = 19842.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118174 restraints weight = 18109.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118287 restraints weight = 14435.155| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 1.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 35242 Z= 0.241 Angle : 0.767 11.319 48089 Z= 0.392 Chirality : 0.050 0.264 5413 Planarity : 0.006 0.066 6155 Dihedral : 6.295 59.520 5420 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.32 % Favored : 92.47 % Rotamer: Outliers : 4.02 % Allowed : 18.56 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4358 helix: 2.09 (0.22), residues: 539 sheet: -0.75 (0.14), residues: 1420 loop : -1.36 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 37 TYR 0.070 0.002 TYR A 93 PHE 0.053 0.002 PHE K 50 TRP 0.028 0.002 TRP G 89 HIS 0.010 0.002 HIS K 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (35144) covalent geometry : angle 0.75673 / 0.39 (47860) SS BOND : bond 0.00455 / 0.30 ( 65) SS BOND : angle 1.71654 / 1.20 ( 130) hydrogen bonds : bond 0.04269 / 2.81 ( 1151) hydrogen bonds : angle 5.07239 / 3.59 ( 3195) link_BETA1-4 : bond 0.00810 / 0.46 ( 22) link_BETA1-4 : angle 1.89189 / 1.25 ( 66) link_NAG-ASN : bond 0.00929 / 0.45 ( 11) link_NAG-ASN : angle 2.67164 / 1.78 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 470 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7783 (tpp-160) REVERT: A 364 SER cc_start: 0.9373 (t) cc_final: 0.9068 (p) REVERT: B 174 ASP cc_start: 0.8477 (p0) cc_final: 0.8175 (p0) REVERT: B 302 ASP cc_start: 0.7822 (p0) cc_final: 0.7523 (p0) REVERT: B 315 GLU cc_start: 0.7854 (tt0) cc_final: 0.7652 (tt0) REVERT: B 387 MET cc_start: 0.6899 (ttm) cc_final: 0.6506 (ttm) REVERT: F 95 PHE cc_start: 0.6667 (t80) cc_final: 0.6405 (t80) REVERT: F 174 ASP cc_start: 0.8301 (t0) cc_final: 0.7829 (t0) REVERT: F 182 ASP cc_start: 0.7873 (p0) cc_final: 0.7670 (t0) REVERT: F 280 MET cc_start: 0.8439 (ptp) cc_final: 0.8065 (ptp) REVERT: F 345 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8355 (ttmm) REVERT: F 384 LYS cc_start: 0.5070 (mptt) cc_final: 0.2596 (mmtm) REVERT: G 16 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7859 (mttm) REVERT: G 89 TRP cc_start: 0.9209 (p-90) cc_final: 0.8966 (p-90) REVERT: G 134 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8402 (ptp90) REVERT: G 147 TYR cc_start: 0.7312 (m-10) cc_final: 0.6855 (m-10) REVERT: G 269 MET cc_start: 0.8351 (mmm) cc_final: 0.8063 (mtm) REVERT: G 280 MET cc_start: 0.9254 (mtm) cc_final: 0.8964 (mtm) REVERT: G 397 VAL cc_start: 0.9125 (t) cc_final: 0.8846 (p) REVERT: H 88 MET cc_start: 0.8628 (mmm) cc_final: 0.8238 (mtt) REVERT: H 269 MET cc_start: 0.8323 (mmm) cc_final: 0.7842 (mmm) REVERT: H 402 MET cc_start: 0.8522 (tpp) cc_final: 0.8321 (mmt) REVERT: I 97 MET cc_start: 0.7810 (ppp) cc_final: 0.7598 (tmm) REVERT: I 304 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: I 373 MET cc_start: 0.7456 (tpp) cc_final: 0.7112 (mtt) REVERT: J 7 ASN cc_start: 0.8215 (t0) cc_final: 0.6981 (t0) REVERT: J 10 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7149 (mtmm) REVERT: J 166 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: K 50 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: K 57 ASP cc_start: 0.7763 (t0) cc_final: 0.7145 (t0) REVERT: N 36 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5701 (mp) REVERT: O 221 ARG cc_start: 0.8860 (mmt-90) cc_final: 0.8653 (tpp-160) REVERT: P 120 ILE cc_start: 0.6956 (pt) cc_final: 0.6732 (mt) REVERT: P 183 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8325 (ptpp) REVERT: Q 111 MET cc_start: 0.8220 (pmm) cc_final: 0.7319 (pmm) REVERT: Q 139 LYS cc_start: 0.5502 (mtmt) cc_final: 0.4943 (pttp) REVERT: Q 161 LYS cc_start: 0.8495 (mttm) cc_final: 0.8254 (ttmm) REVERT: Q 183 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: Q 224 PHE cc_start: 0.8886 (m-80) cc_final: 0.8252 (m-80) REVERT: Q 229 ARG cc_start: 0.7212 (mtm180) cc_final: 0.6910 (mtm180) outliers start: 150 outliers final: 102 residues processed: 588 average time/residue: 0.1998 time to fit residues: 195.5931 Evaluate side-chains 526 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 417 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain K residue 328 HIS Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 185 THR Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 141 MET Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.664 > 50: distance: 12 - 145: 29.093 distance: 15 - 142: 28.526 distance: 72 - 76: 29.664 distance: 76 - 77: 43.879 distance: 77 - 78: 41.332 distance: 77 - 80: 39.257 distance: 78 - 79: 31.752 distance: 78 - 85: 39.596 distance: 79 - 147: 40.625 distance: 80 - 81: 38.792 distance: 81 - 82: 53.854 distance: 82 - 83: 54.637 distance: 82 - 84: 24.606 distance: 85 - 86: 8.210 distance: 86 - 87: 35.657 distance: 86 - 89: 37.068 distance: 87 - 93: 20.139 distance: 89 - 90: 8.001 distance: 89 - 91: 36.287 distance: 90 - 92: 28.737 distance: 93 - 94: 45.199 distance: 93 - 134: 42.464 distance: 94 - 97: 65.716 distance: 95 - 96: 33.293 distance: 95 - 102: 38.050 distance: 96 - 131: 10.468 distance: 97 - 98: 49.246 distance: 98 - 99: 24.594 distance: 99 - 100: 41.746 distance: 100 - 101: 66.748 distance: 102 - 103: 23.345 distance: 103 - 104: 21.927 distance: 103 - 106: 58.965 distance: 104 - 105: 40.361 distance: 106 - 108: 27.275 distance: 110 - 111: 56.962 distance: 110 - 113: 7.052 distance: 111 - 112: 6.263 distance: 111 - 117: 69.963 distance: 113 - 114: 54.094 distance: 114 - 115: 28.250 distance: 114 - 116: 18.225 distance: 117 - 118: 46.701 distance: 117 - 123: 39.660 distance: 118 - 119: 45.929 distance: 118 - 121: 54.463 distance: 119 - 120: 40.654 distance: 119 - 124: 40.482 distance: 121 - 122: 42.044 distance: 122 - 123: 63.877 distance: 124 - 125: 60.677 distance: 125 - 126: 45.572 distance: 125 - 128: 40.667 distance: 126 - 131: 10.169 distance: 128 - 129: 48.853 distance: 128 - 130: 64.322 distance: 131 - 132: 32.264 distance: 132 - 133: 18.672 distance: 132 - 135: 25.330 distance: 133 - 134: 49.340 distance: 133 - 142: 44.549 distance: 135 - 136: 13.442 distance: 136 - 137: 9.546 distance: 137 - 138: 14.949 distance: 138 - 139: 17.681 distance: 139 - 140: 35.623 distance: 139 - 141: 40.908 distance: 142 - 143: 26.356 distance: 143 - 144: 19.158 distance: 143 - 146: 32.466 distance: 144 - 145: 37.076 distance: 144 - 147: 49.035 distance: 147 - 148: 26.779 distance: 148 - 149: 21.213 distance: 148 - 151: 37.994 distance: 149 - 150: 6.309 distance: 149 - 155: 29.487 distance: 151 - 152: 35.936 distance: 152 - 153: 19.559 distance: 153 - 154: 21.568