Starting phenix.real_space_refine on Sun Jun 29 07:46:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw0_39618/06_2025/8yw0_39618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw0_39618/06_2025/8yw0_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_39618/06_2025/8yw0_39618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw0_39618/06_2025/8yw0_39618.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw0_39618/06_2025/8yw0_39618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw0_39618/06_2025/8yw0_39618.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.16, per 1000 atoms: 0.65 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: 11.44 Conformation dependent library (CDL) restraints added in 4.9 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: 8.87 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: 16.69 Time building geometry restraints manager: 11.44 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: 0.03 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: 18.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 11.010 Check model and map are aligned: 0.360 Set scattering table: 0.400 Process input model: 88.650 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4514 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.014 0.001 TRP P 195 HIS 0.016 0.001 HIS D 125 PHE 0.027 0.001 PHE K 50 TYR 0.027 0.001 TYR F 93 ARG 0.011 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 11) link_NAG-ASN : angle 1.68598 ( 33) link_BETA1-4 : bond 0.00785 ( 22) link_BETA1-4 : angle 2.06708 ( 66) hydrogen bonds : bond 0.23712 ( 1151) hydrogen bonds : angle 7.93909 ( 3195) SS BOND : bond 0.00420 ( 65) SS BOND : angle 1.49954 ( 130) covalent geometry : bond 0.00343 (35144) covalent geometry : angle 0.64107 (47860) *********************** 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 : 3.331 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: A 252 ASN cc_start: 0.5404 (m110) cc_final: 0.5136 (m110) REVERT: D 142 LYS cc_start: 0.6563 (ptmm) cc_final: 0.5918 (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: 0.5561 (m-80) REVERT: K 286 LEU cc_start: 0.4393 (mt) cc_final: 0.3573 (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: 0.5840 (mtmt) REVERT: P 161 LYS cc_start: 0.6584 (ttmm) cc_final: 0.5746 (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: 0.4951 time to fit residues: 692.5154 Evaluate side-chains 586 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 338 optimal weight: 0.1980 chunk 131 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 392 optimal weight: 40.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 GLN H 30 GLN J 120 ASN J 131 HIS J 352 HIS K 53 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133794 restraints weight = 47020.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138457 restraints weight = 23203.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139733 restraints weight = 14767.969| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5105 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35242 Z= 0.132 Angle : 0.678 13.940 48089 Z= 0.338 Chirality : 0.046 0.248 5413 Planarity : 0.005 0.073 6155 Dihedral : 9.176 71.426 5420 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Rotamer: Outliers : 2.31 % Allowed : 10.09 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 4358 helix: 2.05 (0.22), residues: 575 sheet: -0.46 (0.14), residues: 1368 loop : -1.29 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 235 HIS 0.011 0.001 HIS D 176 PHE 0.018 0.001 PHE P 207 TYR 0.025 0.002 TYR A 85 ARG 0.011 0.001 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 11) link_NAG-ASN : angle 1.43703 ( 33) link_BETA1-4 : bond 0.00658 ( 22) link_BETA1-4 : angle 2.69825 ( 66) hydrogen bonds : bond 0.03721 ( 1151) hydrogen bonds : angle 5.56649 ( 3195) SS BOND : bond 0.00547 ( 65) SS BOND : angle 1.05529 ( 130) covalent geometry : bond 0.00285 (35144) covalent geometry : angle 0.66935 (47860) *********************** 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 717 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 631 time to evaluate : 3.423 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: 0.5715 (t70) cc_final: 0.4461 (t0) REVERT: A 384 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7633 (mmtm) REVERT: D 141 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7045 (mtt) REVERT: F 88 MET cc_start: 0.6205 (mmm) cc_final: 0.5873 (mmm) REVERT: H 163 PHE cc_start: 0.6820 (m-80) cc_final: 0.6564 (m-80) REVERT: I 169 MET cc_start: 0.5512 (mmm) cc_final: 0.5066 (mmm) REVERT: J 8 VAL cc_start: 0.4798 (OUTLIER) cc_final: 0.4461 (t) REVERT: J 358 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4917 (t80) REVERT: J 373 MET cc_start: 0.5356 (mmt) cc_final: 0.5064 (mmt) REVERT: K 169 MET cc_start: 0.7267 (mmt) cc_final: 0.6996 (mmm) REVERT: K 358 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.6235 (t80) REVERT: M 38 MET cc_start: 0.8176 (tmm) cc_final: 0.7946 (tmm) REVERT: M 39 LEU cc_start: 0.6774 (mt) cc_final: 0.6064 (mt) REVERT: M 48 TYR cc_start: 0.4318 (t80) cc_final: 0.4058 (t80) REVERT: N 35 THR cc_start: 0.7306 (m) cc_final: 0.6886 (p) REVERT: N 48 TYR cc_start: 0.4939 (t80) cc_final: 0.4219 (t80) REVERT: O 221 ARG cc_start: 0.6343 (tpp-160) cc_final: 0.6054 (ttm110) REVERT: O 240 GLU cc_start: 0.6116 (tm-30) cc_final: 0.5594 (pm20) REVERT: P 128 LYS cc_start: 0.7045 (mmmt) cc_final: 0.6750 (mmmm) REVERT: P 139 LYS cc_start: 0.6066 (mttm) cc_final: 0.5621 (mtmt) REVERT: P 161 LYS cc_start: 0.6993 (ttmm) cc_final: 0.6256 (ttpt) REVERT: P 224 PHE cc_start: 0.4867 (m-80) cc_final: 0.4607 (m-80) outliers start: 86 outliers final: 44 residues processed: 670 average time/residue: 0.4455 time to fit residues: 501.0060 Evaluate side-chains 594 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 546 time to evaluate : 3.576 ------------------------------------------------------------------------------- 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 148 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 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 8 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 358 TYR 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 282 VAL 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 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 360 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 357 optimal weight: 50.0000 chunk 267 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 315 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 32 GLN A 235 GLN B 53 GLN B 131 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN B 255 HIS B 340 GLN D 176 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS G 118 HIS H 18 HIS H 270 ASN H 325 ASN H 331 HIS H 394 HIS I 53 GLN I 77 ASN I 236 GLN I 290 HIS ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN ** J 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 GLN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 340 GLN K 348 HIS O 197 HIS ** Q 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147963 restraints weight = 49069.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150059 restraints weight = 24814.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151009 restraints weight = 15350.213| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.9817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.174 35242 Z= 0.341 Angle : 1.045 16.630 48089 Z= 0.549 Chirality : 0.059 0.451 5413 Planarity : 0.008 0.089 6155 Dihedral : 7.812 58.516 5420 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.85 % Favored : 91.83 % Rotamer: Outliers : 5.04 % Allowed : 13.22 % Favored : 81.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4358 helix: 1.26 (0.21), residues: 575 sheet: -0.73 (0.15), residues: 1084 loop : -1.79 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP J 329 HIS 0.083 0.003 HIS P 176 PHE 0.048 0.004 PHE I 92 TYR 0.040 0.003 TYR A 85 ARG 0.021 0.001 ARG J 266 Details of bonding type rmsd link_NAG-ASN : bond 0.00872 ( 11) link_NAG-ASN : angle 2.96441 ( 33) link_BETA1-4 : bond 0.00841 ( 22) link_BETA1-4 : angle 2.29624 ( 66) hydrogen bonds : bond 0.05799 ( 1151) hydrogen bonds : angle 6.30480 ( 3195) SS BOND : bond 0.01643 ( 65) SS BOND : angle 1.91349 ( 130) covalent geometry : bond 0.00785 (35144) covalent geometry : angle 1.03641 (47860) *********************** 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 934 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 746 time to evaluate : 3.744 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: A 35 GLU cc_start: 0.7755 (tt0) cc_final: 0.7479 (tt0) REVERT: A 261 ILE cc_start: 0.9245 (mm) cc_final: 0.9037 (mm) REVERT: A 345 LYS cc_start: 0.7577 (mtpp) cc_final: 0.7184 (mtpp) REVERT: B 387 MET cc_start: 0.6560 (ttm) cc_final: 0.5952 (ttp) REVERT: D 141 MET cc_start: 0.8320 (mtt) cc_final: 0.8066 (mtt) REVERT: D 249 VAL cc_start: 0.7910 (t) cc_final: 0.7700 (t) REVERT: F 156 ILE cc_start: 0.8927 (mt) cc_final: 0.8703 (mt) REVERT: F 299 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8113 (tp) REVERT: F 302 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7476 (p) REVERT: G 16 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7817 (mttm) REVERT: G 397 VAL cc_start: 0.8957 (t) cc_final: 0.8703 (p) REVERT: H 88 MET cc_start: 0.8718 (mmm) cc_final: 0.8355 (mtt) REVERT: I 76 GLU cc_start: 0.6981 (mp0) cc_final: 0.6476 (pm20) REVERT: I 77 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6980 (p0) REVERT: I 171 MET cc_start: 0.7700 (mmm) cc_final: 0.7460 (mmm) REVERT: I 307 GLU cc_start: 0.8310 (pm20) cc_final: 0.7979 (pt0) REVERT: I 373 MET cc_start: 0.7269 (tpp) cc_final: 0.6968 (mtt) REVERT: J 53 GLN cc_start: 0.8108 (pt0) cc_final: 0.7889 (mt0) REVERT: J 331 ASN cc_start: 0.6936 (m110) cc_final: 0.6669 (t0) REVERT: K 45 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8174 (mmt) REVERT: K 128 GLN cc_start: 0.7365 (pp30) cc_final: 0.6744 (pt0) REVERT: K 174 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7191 (p0) REVERT: K 259 PRO cc_start: 0.7322 (Cg_exo) cc_final: 0.7000 (Cg_endo) REVERT: N 36 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6213 (mp) REVERT: O 218 ASP cc_start: 0.6340 (t70) cc_final: 0.6057 (t0) REVERT: O 251 TRP cc_start: 0.8774 (p90) cc_final: 0.8505 (p90) REVERT: P 120 ILE cc_start: 0.6042 (pt) cc_final: 0.5802 (pt) REVERT: Q 161 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8499 (mtpp) outliers start: 188 outliers final: 71 residues processed: 885 average time/residue: 0.4181 time to fit residues: 616.0646 Evaluate side-chains 611 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 533 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 299 LEU 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 230 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 259 CYS 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 330 VAL Chi-restraints excluded: chain H residue 366 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 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 379 ILE 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 272 GLU Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 45 MET 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 150 GLU Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 328 HIS 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 K residue 401 LEU 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 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 HIS 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 257 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 104 optimal weight: 0.0970 chunk 303 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 53 GLN B 236 GLN B 255 HIS B 340 GLN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 ASN I 120 ASN I 170 HIS I 290 HIS I 340 GLN I 352 HIS J 73 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 HIS J 352 HIS K 53 GLN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 340 GLN P 176 HIS Q 196 HIS T 199 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131621 restraints weight = 48141.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134269 restraints weight = 22608.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133854 restraints weight = 15986.455| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 1.0222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35242 Z= 0.152 Angle : 0.708 23.032 48089 Z= 0.357 Chirality : 0.047 0.286 5413 Planarity : 0.005 0.077 6155 Dihedral : 6.565 59.825 5420 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 3.35 % Allowed : 17.41 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4358 helix: 2.18 (0.22), residues: 531 sheet: -0.64 (0.14), residues: 1300 loop : -1.50 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 235 HIS 0.009 0.001 HIS I 130 PHE 0.019 0.001 PHE K 50 TYR 0.021 0.001 TYR K 357 ARG 0.009 0.001 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 11) link_NAG-ASN : angle 5.32842 ( 33) link_BETA1-4 : bond 0.00811 ( 22) link_BETA1-4 : angle 2.22376 ( 66) hydrogen bonds : bond 0.03713 ( 1151) hydrogen bonds : angle 5.35716 ( 3195) SS BOND : bond 0.00280 ( 65) SS BOND : angle 1.83304 ( 130) covalent geometry : bond 0.00349 (35144) covalent geometry : angle 0.68408 (47860) *********************** 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 661 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 536 time to evaluate : 3.347 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: A 140 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8707 (t) REVERT: A 142 GLN cc_start: 0.8765 (mt0) cc_final: 0.8549 (mt0) REVERT: A 345 LYS cc_start: 0.7652 (mtpp) cc_final: 0.7261 (mtpp) REVERT: B 7 ASN cc_start: 0.7371 (t0) cc_final: 0.7129 (t0) REVERT: B 251 LYS cc_start: 0.8163 (tptm) cc_final: 0.7807 (tptp) REVERT: B 301 GLU cc_start: 0.7794 (tp30) cc_final: 0.7515 (tt0) REVERT: B 373 MET cc_start: 0.8048 (ttp) cc_final: 0.7822 (mtm) REVERT: B 387 MET cc_start: 0.6619 (ttm) cc_final: 0.6137 (ttm) REVERT: F 285 SER cc_start: 0.9098 (m) cc_final: 0.8674 (t) REVERT: F 302 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7534 (p) REVERT: G 16 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7396 (ptpp) REVERT: G 99 GLU cc_start: 0.7476 (mp0) cc_final: 0.7050 (tm-30) REVERT: G 246 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7192 (tm-30) REVERT: G 397 VAL cc_start: 0.8830 (t) cc_final: 0.8560 (p) REVERT: H 88 MET cc_start: 0.8846 (mmm) cc_final: 0.8271 (mtt) REVERT: H 385 ASP cc_start: 0.7432 (t0) cc_final: 0.7138 (m-30) REVERT: H 402 MET cc_start: 0.8089 (mmt) cc_final: 0.7843 (mmt) REVERT: I 71 ASP cc_start: 0.7746 (p0) cc_final: 0.7464 (p0) REVERT: I 96 THR cc_start: 0.6277 (m) cc_final: 0.5937 (p) REVERT: I 307 GLU cc_start: 0.8313 (pm20) cc_final: 0.8048 (pt0) REVERT: I 376 LEU cc_start: 0.8130 (tp) cc_final: 0.7817 (tt) REVERT: K 128 GLN cc_start: 0.7426 (pp30) cc_final: 0.7109 (pt0) REVERT: K 328 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7117 (t-90) REVERT: M 18 CYS cc_start: 0.5149 (m) cc_final: 0.4769 (m) REVERT: O 251 TRP cc_start: 0.9000 (p90) cc_final: 0.8602 (p90) REVERT: P 128 LYS cc_start: 0.6984 (mmmt) cc_final: 0.6746 (mmmm) outliers start: 125 outliers final: 68 residues processed: 622 average time/residue: 0.4339 time to fit residues: 452.4184 Evaluate side-chains 562 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 490 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 THR 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 19 ILE Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 376 CYS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 328 HIS Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 232 HIS 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 379 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 8 MET 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 141 MET Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 255 MET 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 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 242 optimal weight: 0.3980 chunk 428 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 176 optimal weight: 0.4980 chunk 320 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 268 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS D 176 HIS D 186 HIS F 230 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN I 77 ASN I 130 HIS I 170 HIS J 73 HIS J 77 ASN J 157 GLN J 255 HIS J 348 HIS J 352 HIS K 226 HIS K 238 ASN K 328 HIS ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS Q 197 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.180752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137379 restraints weight = 47066.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139324 restraints weight = 24091.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139214 restraints weight = 15940.496| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 1.0374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 35242 Z= 0.109 Angle : 0.621 17.905 48089 Z= 0.310 Chirality : 0.045 0.379 5413 Planarity : 0.005 0.055 6155 Dihedral : 5.850 59.874 5420 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.78 % Favored : 94.01 % Rotamer: Outliers : 3.30 % Allowed : 18.13 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4358 helix: 2.44 (0.23), residues: 531 sheet: -0.47 (0.14), residues: 1284 loop : -1.32 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 89 HIS 0.010 0.001 HIS H 308 PHE 0.016 0.001 PHE J 50 TYR 0.017 0.001 TYR G 233 ARG 0.005 0.000 ARG J 138 Details of bonding type rmsd link_NAG-ASN : bond 0.01385 ( 11) link_NAG-ASN : angle 4.84470 ( 33) link_BETA1-4 : bond 0.00603 ( 22) link_BETA1-4 : angle 1.91471 ( 66) hydrogen bonds : bond 0.03172 ( 1151) hydrogen bonds : angle 4.93363 ( 3195) SS BOND : bond 0.00468 ( 65) SS BOND : angle 1.33347 ( 130) covalent geometry : bond 0.00244 (35144) covalent geometry : angle 0.60168 (47860) *********************** 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 651 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 528 time to evaluate : 3.785 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: A 80 VAL cc_start: 0.9071 (m) cc_final: 0.8824 (t) REVERT: A 115 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7848 (ptt90) REVERT: A 142 GLN cc_start: 0.8629 (mt0) cc_final: 0.8385 (mt0) REVERT: A 269 MET cc_start: 0.7517 (ttp) cc_final: 0.7250 (ttm) REVERT: B 251 LYS cc_start: 0.8051 (tptm) cc_final: 0.7684 (tptp) REVERT: B 387 MET cc_start: 0.6766 (ttm) cc_final: 0.6300 (ttm) REVERT: F 285 SER cc_start: 0.9018 (m) cc_final: 0.8651 (t) REVERT: F 302 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7386 (p) REVERT: G 16 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7442 (ptpp) REVERT: G 99 GLU cc_start: 0.7456 (mp0) cc_final: 0.7093 (tm-30) REVERT: G 246 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7226 (tm-30) REVERT: G 402 MET cc_start: 0.7932 (mmm) cc_final: 0.7571 (mmt) REVERT: H 402 MET cc_start: 0.8036 (mmt) cc_final: 0.7822 (mmt) REVERT: J 91 CYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7195 (m) REVERT: K 128 GLN cc_start: 0.7329 (pp30) cc_final: 0.7092 (pt0) REVERT: M 18 CYS cc_start: 0.5228 (m) cc_final: 0.4859 (m) REVERT: N 36 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5751 (mp) REVERT: O 227 LYS cc_start: 0.8538 (mptt) cc_final: 0.8310 (mmtp) REVERT: O 251 TRP cc_start: 0.8890 (p90) cc_final: 0.8500 (p90) REVERT: P 141 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7154 (mtm) REVERT: Q 139 LYS cc_start: 0.5649 (mtmt) cc_final: 0.5317 (pttp) outliers start: 123 outliers final: 78 residues processed: 613 average time/residue: 0.4227 time to fit residues: 437.9902 Evaluate side-chains 545 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 462 time to evaluate : 3.404 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL 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 C residue 8 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 376 CYS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 ARG 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 352 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 THR 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 388 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 305 TYR 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 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 141 MET Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 255 MET 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 249 VAL Chi-restraints excluded: chain Q residue 257 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 195 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 422 optimal weight: 8.9990 chunk 402 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 306 optimal weight: 0.0870 chunk 222 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 134 GLN F 32 GLN F 333 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 HIS I 120 ASN I 170 HIS J 53 GLN J 73 HIS J 255 HIS J 331 ASN J 352 HIS K 238 ASN K 340 GLN L 31 ASN O 197 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123702 restraints weight = 46602.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124724 restraints weight = 24940.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124654 restraints weight = 18039.729| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 1.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 35242 Z= 0.190 Angle : 0.712 20.048 48089 Z= 0.356 Chirality : 0.048 0.431 5413 Planarity : 0.005 0.064 6155 Dihedral : 6.085 59.258 5420 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.72 % Favored : 93.05 % Rotamer: Outliers : 4.21 % Allowed : 17.97 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4358 helix: 2.39 (0.22), residues: 531 sheet: -0.53 (0.14), residues: 1336 loop : -1.34 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP G 89 HIS 0.013 0.002 HIS K 328 PHE 0.026 0.002 PHE I 50 TYR 0.029 0.002 TYR A 93 ARG 0.008 0.001 ARG K 138 Details of bonding type rmsd link_NAG-ASN : bond 0.01694 ( 11) link_NAG-ASN : angle 5.28040 ( 33) link_BETA1-4 : bond 0.01505 ( 22) link_BETA1-4 : angle 2.63403 ( 66) hydrogen bonds : bond 0.03820 ( 1151) hydrogen bonds : angle 4.91597 ( 3195) SS BOND : bond 0.00325 ( 65) SS BOND : angle 1.63309 ( 130) covalent geometry : bond 0.00455 (35144) covalent geometry : angle 0.68753 (47860) *********************** 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 662 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 505 time to evaluate : 3.527 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: A 115 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8158 (ttp80) REVERT: A 186 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8837 (m-40) REVERT: A 269 MET cc_start: 0.7819 (ttp) cc_final: 0.7594 (ttm) REVERT: B 224 GLN cc_start: 0.7395 (mt0) cc_final: 0.7153 (tp40) REVERT: B 251 LYS cc_start: 0.8424 (tptm) cc_final: 0.7876 (tptp) REVERT: B 387 MET cc_start: 0.6817 (ttm) cc_final: 0.6397 (ttm) REVERT: D 182 SER cc_start: 0.8926 (m) cc_final: 0.8716 (p) REVERT: F 174 ASP cc_start: 0.8376 (t0) cc_final: 0.7961 (t0) REVERT: F 208 VAL cc_start: 0.8898 (m) cc_final: 0.8629 (p) REVERT: F 285 SER cc_start: 0.9201 (m) cc_final: 0.8931 (t) REVERT: F 345 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8438 (ttmm) REVERT: F 384 LYS cc_start: 0.4853 (mptt) cc_final: 0.2623 (mmtm) REVERT: G 16 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7799 (mttm) REVERT: H 88 MET cc_start: 0.8792 (mmm) cc_final: 0.8138 (mtt) REVERT: H 269 MET cc_start: 0.8118 (mmm) cc_final: 0.7501 (mmm) REVERT: H 402 MET cc_start: 0.7980 (mmt) cc_final: 0.7774 (mmt) REVERT: K 50 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: K 128 GLN cc_start: 0.7448 (pp30) cc_final: 0.7201 (tt0) REVERT: K 356 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7988 (mt0) REVERT: L 35 THR cc_start: 0.7100 (m) cc_final: 0.6900 (m) REVERT: N 36 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5486 (mp) REVERT: O 165 LYS cc_start: 0.8736 (tttp) cc_final: 0.8464 (tttm) REVERT: O 229 ARG cc_start: 0.7158 (mtm180) cc_final: 0.6888 (mtm180) REVERT: O 251 TRP cc_start: 0.8994 (p90) cc_final: 0.8759 (p90) REVERT: Q 139 LYS cc_start: 0.5489 (mtmt) cc_final: 0.5164 (pttp) REVERT: Q 183 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7761 (mtpt) outliers start: 157 outliers final: 98 residues processed: 617 average time/residue: 0.5266 time to fit residues: 550.4234 Evaluate side-chains 554 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 451 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 186 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 325 ASN Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 53 GLN 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 298 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 244 LEU 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 376 CYS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 360 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 318 ILE 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 M residue 8 MET 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 192 HIS 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 242 SER Chi-restraints excluded: chain P residue 255 MET 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 249 VAL Chi-restraints excluded: chain Q residue 257 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 33 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 171 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 230 HIS ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN I 120 ASN I 170 HIS J 53 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 352 HIS K 255 HIS K 306 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125810 restraints weight = 46571.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125742 restraints weight = 25944.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126574 restraints weight = 18191.644| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 1.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35242 Z= 0.131 Angle : 0.641 19.404 48089 Z= 0.322 Chirality : 0.045 0.446 5413 Planarity : 0.005 0.058 6155 Dihedral : 5.767 59.678 5420 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.71 % Favored : 94.08 % Rotamer: Outliers : 3.27 % Allowed : 19.37 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4358 helix: 2.54 (0.23), residues: 531 sheet: -0.46 (0.14), residues: 1296 loop : -1.23 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 89 HIS 0.007 0.001 HIS J 352 PHE 0.018 0.001 PHE K 50 TYR 0.024 0.001 TYR A 76 ARG 0.006 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01219 ( 11) link_NAG-ASN : angle 4.91632 ( 33) link_BETA1-4 : bond 0.00725 ( 22) link_BETA1-4 : angle 1.82493 ( 66) hydrogen bonds : bond 0.03284 ( 1151) hydrogen bonds : angle 4.72081 ( 3195) SS BOND : bond 0.00236 ( 65) SS BOND : angle 1.32518 ( 130) covalent geometry : bond 0.00304 (35144) covalent geometry : angle 0.62226 (47860) *********************** 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 590 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 468 time to evaluate : 3.692 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: A 298 ASP cc_start: 0.6986 (t70) cc_final: 0.6716 (t0) REVERT: B 174 ASP cc_start: 0.8571 (p0) cc_final: 0.8196 (p0) REVERT: B 224 GLN cc_start: 0.7841 (mt0) cc_final: 0.7594 (tt0) REVERT: B 251 LYS cc_start: 0.8489 (tptm) cc_final: 0.7962 (tptp) REVERT: B 325 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7691 (pmm) REVERT: B 387 MET cc_start: 0.6830 (ttm) cc_final: 0.6254 (ttp) REVERT: F 174 ASP cc_start: 0.8329 (t0) cc_final: 0.7890 (t0) REVERT: F 384 LYS cc_start: 0.5017 (mptt) cc_final: 0.2764 (mmtm) REVERT: G 3 HIS cc_start: 0.8449 (t-90) cc_final: 0.8056 (t-170) REVERT: G 16 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7807 (mttm) REVERT: H 269 MET cc_start: 0.8235 (mmm) cc_final: 0.7522 (mmm) REVERT: H 432 THR cc_start: 0.6665 (t) cc_final: 0.6315 (t) REVERT: K 57 ASP cc_start: 0.7372 (t0) cc_final: 0.6893 (t0) REVERT: K 166 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7663 (mt-10) REVERT: K 224 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7368 (mm-40) REVERT: L 35 THR cc_start: 0.7307 (m) cc_final: 0.7094 (m) REVERT: N 36 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5676 (mp) REVERT: O 165 LYS cc_start: 0.8770 (tttp) cc_final: 0.8501 (tttm) REVERT: O 229 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6930 (mtm180) REVERT: Q 139 LYS cc_start: 0.5466 (mtmt) cc_final: 0.5096 (pttp) REVERT: Q 183 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7815 (mtpt) outliers start: 122 outliers final: 89 residues processed: 559 average time/residue: 0.4569 time to fit residues: 427.3012 Evaluate side-chains 527 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 434 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS 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 280 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 255 HIS 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 325 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 CYS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 360 SER Chi-restraints excluded: chain H residue 366 VAL 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 361 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 53 GLN 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 256 ILE Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 305 TYR 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 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 P residue 175 VAL Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 255 MET 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 249 VAL Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 88 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 274 optimal weight: 0.0040 chunk 135 optimal weight: 3.9990 chunk 427 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 396 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 134 GLN J 53 GLN J 352 HIS K 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122052 restraints weight = 46435.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122248 restraints weight = 24920.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122868 restraints weight = 17296.087| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 1.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35242 Z= 0.152 Angle : 0.658 19.382 48089 Z= 0.330 Chirality : 0.046 0.464 5413 Planarity : 0.005 0.056 6155 Dihedral : 5.796 59.303 5420 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.45 % Favored : 93.37 % Rotamer: Outliers : 3.22 % Allowed : 20.06 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4358 helix: 2.49 (0.23), residues: 535 sheet: -0.51 (0.14), residues: 1308 loop : -1.22 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 89 HIS 0.007 0.001 HIS I 232 PHE 0.027 0.001 PHE K 50 TYR 0.024 0.001 TYR A 76 ARG 0.007 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00999 ( 11) link_NAG-ASN : angle 5.03049 ( 33) link_BETA1-4 : bond 0.00603 ( 22) link_BETA1-4 : angle 1.83738 ( 66) hydrogen bonds : bond 0.03430 ( 1151) hydrogen bonds : angle 4.69984 ( 3195) SS BOND : bond 0.00480 ( 65) SS BOND : angle 1.38204 ( 130) covalent geometry : bond 0.00363 (35144) covalent geometry : angle 0.63809 (47860) *********************** REFINEMENT MACRO_CYCLE 8 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 573 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 453 time to evaluate : 3.853 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: A 88 MET cc_start: 0.8570 (mtp) cc_final: 0.8268 (mtp) REVERT: A 289 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7726 (tpp-160) REVERT: A 298 ASP cc_start: 0.7146 (t70) cc_final: 0.6755 (t0) REVERT: B 174 ASP cc_start: 0.8565 (p0) cc_final: 0.8203 (p0) REVERT: B 224 GLN cc_start: 0.8023 (mt0) cc_final: 0.7727 (tt0) REVERT: B 251 LYS cc_start: 0.8563 (tptm) cc_final: 0.8143 (tppt) REVERT: B 305 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: B 387 MET cc_start: 0.6873 (ttm) cc_final: 0.6298 (ttp) REVERT: D 190 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: F 174 ASP cc_start: 0.8359 (t0) cc_final: 0.7927 (t0) REVERT: F 384 LYS cc_start: 0.5026 (mptt) cc_final: 0.2663 (mmtm) REVERT: G 16 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7851 (mttm) REVERT: G 246 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7483 (tm-30) REVERT: G 320 TYR cc_start: 0.8552 (p90) cc_final: 0.8303 (p90) REVERT: H 134 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8137 (ptm160) REVERT: H 136 MET cc_start: 0.8510 (ptp) cc_final: 0.8128 (ptm) REVERT: H 269 MET cc_start: 0.8157 (mmm) cc_final: 0.7538 (mmm) REVERT: I 166 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7603 (mm-30) REVERT: J 253 LYS cc_start: 0.9118 (ptpt) cc_final: 0.8914 (ptpt) REVERT: K 166 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7764 (mt-10) REVERT: K 224 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7363 (mm-40) REVERT: L 35 THR cc_start: 0.7467 (m) cc_final: 0.7235 (m) REVERT: N 36 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5507 (mp) REVERT: O 165 LYS cc_start: 0.8827 (tttp) cc_final: 0.8559 (tttm) REVERT: O 229 ARG cc_start: 0.7134 (mtm180) cc_final: 0.6847 (mtm180) REVERT: Q 139 LYS cc_start: 0.5453 (mtmt) cc_final: 0.5116 (pttm) REVERT: Q 183 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7951 (mtpt) outliers start: 120 outliers final: 92 residues processed: 544 average time/residue: 0.5255 time to fit residues: 479.1137 Evaluate side-chains 527 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 429 time to evaluate : 5.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 82 THR 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 280 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 254 VAL 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 C residue 8 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 134 ARG 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 317 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 360 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 85 VAL 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 361 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 53 GLN 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 256 ILE Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 315 GLU 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 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 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 255 MET 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 249 VAL Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 244 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 357 optimal weight: 0.0770 chunk 336 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 overall best weight: 2.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 238 ASN B 255 HIS G 118 HIS J 53 GLN J 352 HIS K 255 HIS Q 196 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.165893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119676 restraints weight = 46356.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120320 restraints weight = 24407.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120763 restraints weight = 16608.000| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 1.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35242 Z= 0.165 Angle : 0.671 19.262 48089 Z= 0.337 Chirality : 0.047 0.466 5413 Planarity : 0.005 0.055 6155 Dihedral : 5.938 59.590 5420 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.03 % Favored : 93.76 % Rotamer: Outliers : 3.46 % Allowed : 19.85 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4358 helix: 2.31 (0.23), residues: 539 sheet: -0.52 (0.14), residues: 1308 loop : -1.21 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 89 HIS 0.007 0.001 HIS J 352 PHE 0.049 0.001 PHE F 95 TYR 0.025 0.002 TYR A 76 ARG 0.011 0.000 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00970 ( 11) link_NAG-ASN : angle 5.36272 ( 33) link_BETA1-4 : bond 0.00635 ( 22) link_BETA1-4 : angle 1.81966 ( 66) hydrogen bonds : bond 0.03504 ( 1151) hydrogen bonds : angle 4.74259 ( 3195) SS BOND : bond 0.00309 ( 65) SS BOND : angle 1.31936 ( 130) covalent geometry : bond 0.00398 (35144) covalent geometry : angle 0.65015 (47860) *********************** REFINEMENT MACRO_CYCLE 9 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 583 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 454 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8440 (mmtp) REVERT: A 88 MET cc_start: 0.8643 (mtp) cc_final: 0.8384 (mtp) REVERT: A 115 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7906 (ptt90) REVERT: A 289 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7754 (tpp-160) REVERT: A 298 ASP cc_start: 0.7271 (t70) cc_final: 0.6876 (t0) REVERT: B 174 ASP cc_start: 0.8586 (p0) cc_final: 0.8230 (p0) REVERT: B 224 GLN cc_start: 0.8035 (mt0) cc_final: 0.7758 (tt0) REVERT: B 251 LYS cc_start: 0.8661 (tptm) cc_final: 0.8284 (tppt) REVERT: B 305 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: B 387 MET cc_start: 0.6923 (ttm) cc_final: 0.6327 (ttp) REVERT: D 190 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: D 193 TYR cc_start: 0.8008 (m-80) cc_final: 0.7617 (m-80) REVERT: F 174 ASP cc_start: 0.8349 (t0) cc_final: 0.7916 (t0) REVERT: F 384 LYS cc_start: 0.5115 (mptt) cc_final: 0.2660 (mmtm) REVERT: G 99 GLU cc_start: 0.8220 (mp0) cc_final: 0.7981 (mp0) REVERT: G 246 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7412 (tm-30) REVERT: G 315 VAL cc_start: 0.9116 (m) cc_final: 0.8700 (p) REVERT: H 134 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8140 (ptm160) REVERT: H 136 MET cc_start: 0.8579 (ptp) cc_final: 0.8211 (ptm) REVERT: H 269 MET cc_start: 0.8105 (mmm) cc_final: 0.7535 (mmm) REVERT: I 166 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7493 (mm-30) REVERT: I 196 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7661 (tttp) REVERT: I 325 MET cc_start: 0.9094 (ppp) cc_final: 0.8122 (ppp) REVERT: J 9 TYR cc_start: 0.8291 (m-80) cc_final: 0.7935 (m-80) REVERT: J 53 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: K 166 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7818 (mt-10) REVERT: K 224 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7557 (mm-40) REVERT: L 35 THR cc_start: 0.7626 (m) cc_final: 0.7388 (m) REVERT: N 36 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5569 (mp) REVERT: O 165 LYS cc_start: 0.8964 (tttp) cc_final: 0.8700 (tttm) REVERT: O 229 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6977 (mtm180) REVERT: Q 139 LYS cc_start: 0.5490 (mtmt) cc_final: 0.4864 (pttp) outliers start: 129 outliers final: 99 residues processed: 550 average time/residue: 0.4540 time to fit residues: 415.5351 Evaluate side-chains 533 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 427 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 CYS 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 280 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 254 VAL 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 C residue 8 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 134 ARG 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 317 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 360 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 196 LYS 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 53 GLN 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 256 ILE Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 315 GLU 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 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 183 LYS 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 175 VAL Chi-restraints excluded: chain P residue 185 THR Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 255 MET Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 257 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 170 optimal weight: 0.6980 chunk 273 optimal weight: 0.0980 chunk 217 optimal weight: 0.2980 chunk 159 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 202 optimal weight: 0.4980 chunk 250 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 134 GLN B 255 HIS B 356 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 GLN J 53 GLN P 196 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.169462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123874 restraints weight = 46018.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124215 restraints weight = 24102.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124772 restraints weight = 17554.172| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 1.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 35242 Z= 0.112 Angle : 0.636 18.257 48089 Z= 0.319 Chirality : 0.045 0.456 5413 Planarity : 0.005 0.057 6155 Dihedral : 5.722 59.675 5420 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 2.33 % Allowed : 21.35 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4358 helix: 2.46 (0.23), residues: 539 sheet: -0.41 (0.14), residues: 1296 loop : -1.14 (0.13), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 89 HIS 0.009 0.001 HIS B 226 PHE 0.039 0.001 PHE F 95 TYR 0.025 0.001 TYR A 76 ARG 0.012 0.000 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01017 ( 11) link_NAG-ASN : angle 5.01412 ( 33) link_BETA1-4 : bond 0.00639 ( 22) link_BETA1-4 : angle 1.73879 ( 66) hydrogen bonds : bond 0.03057 ( 1151) hydrogen bonds : angle 4.60236 ( 3195) SS BOND : bond 0.00333 ( 65) SS BOND : angle 1.30145 ( 130) covalent geometry : bond 0.00254 (35144) covalent geometry : angle 0.61633 (47860) ********************** REFINEMENT MACRO_CYCLE 10 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 525 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 438 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8392 (mmtp) REVERT: A 115 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7727 (ptt90) REVERT: A 298 ASP cc_start: 0.7221 (t70) cc_final: 0.6865 (t0) REVERT: B 174 ASP cc_start: 0.8598 (p0) cc_final: 0.8186 (p0) REVERT: B 251 LYS cc_start: 0.8635 (tptm) cc_final: 0.8283 (tppt) REVERT: B 305 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6091 (m-80) REVERT: B 387 MET cc_start: 0.6892 (ttm) cc_final: 0.6282 (ttp) REVERT: D 190 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: D 193 TYR cc_start: 0.7941 (m-80) cc_final: 0.7594 (m-80) REVERT: F 174 ASP cc_start: 0.8301 (t0) cc_final: 0.7853 (t0) REVERT: F 384 LYS cc_start: 0.4992 (mptt) cc_final: 0.2591 (mmtm) REVERT: G 315 VAL cc_start: 0.9075 (m) cc_final: 0.8668 (p) REVERT: H 134 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (ptm160) REVERT: H 136 MET cc_start: 0.8525 (ptp) cc_final: 0.8227 (ptm) REVERT: H 269 MET cc_start: 0.8018 (mmm) cc_final: 0.7419 (mmm) REVERT: I 166 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7420 (mm-30) REVERT: I 196 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7666 (tttp) REVERT: K 166 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7759 (mt-10) REVERT: L 35 THR cc_start: 0.7556 (m) cc_final: 0.7321 (m) REVERT: O 165 LYS cc_start: 0.8922 (tttp) cc_final: 0.8671 (tttm) REVERT: Q 111 MET cc_start: 0.7576 (pmm) cc_final: 0.7214 (pmm) REVERT: Q 139 LYS cc_start: 0.5348 (mtmt) cc_final: 0.4393 (mttp) REVERT: Q 224 PHE cc_start: 0.8691 (m-80) cc_final: 0.8338 (m-80) outliers start: 87 outliers final: 70 residues processed: 498 average time/residue: 0.4257 time to fit residues: 353.7756 Evaluate side-chains 497 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 422 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 360 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 53 GLN 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 256 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 305 TYR 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 M residue 8 MET Chi-restraints excluded: chain N residue 8 MET 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 175 VAL Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain P residue 255 MET Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 97 optimal weight: 0.0770 chunk 205 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN J 53 GLN K 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120316 restraints weight = 46056.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121178 restraints weight = 25456.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122109 restraints weight = 16915.153| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 1.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35242 Z= 0.140 Angle : 0.648 18.704 48089 Z= 0.325 Chirality : 0.045 0.481 5413 Planarity : 0.005 0.056 6155 Dihedral : 5.684 59.419 5420 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.29 % Favored : 93.53 % Rotamer: Outliers : 2.71 % Allowed : 20.55 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4358 helix: 2.31 (0.22), residues: 571 sheet: -0.43 (0.15), residues: 1236 loop : -1.18 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 89 HIS 0.010 0.001 HIS B 226 PHE 0.042 0.001 PHE F 95 TYR 0.024 0.001 TYR A 76 ARG 0.012 0.000 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00989 ( 11) link_NAG-ASN : angle 4.99028 ( 33) link_BETA1-4 : bond 0.00644 ( 22) link_BETA1-4 : angle 1.73116 ( 66) hydrogen bonds : bond 0.03299 ( 1151) hydrogen bonds : angle 4.63348 ( 3195) SS BOND : bond 0.00309 ( 65) SS BOND : angle 1.40343 ( 130) covalent geometry : bond 0.00337 (35144) covalent geometry : angle 0.62913 (47860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15423.22 seconds wall clock time: 273 minutes 18.79 seconds (16398.79 seconds total)