Starting phenix.real_space_refine on Fri May 30 08:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvy_39616/05_2025/8yvy_39616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvy_39616/05_2025/8yvy_39616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yvy_39616/05_2025/8yvy_39616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvy_39616/05_2025/8yvy_39616.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvy_39616/05_2025/8yvy_39616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvy_39616/05_2025/8yvy_39616.cif" } resolution = 3.02 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= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 268 5.16 5 C 21056 2.51 5 N 5748 2.21 5 O 6352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33424 Number of models: 1 Model: "" Number of chains: 28 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: 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: "R" 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: "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: "T" 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 Time building chain proxies: 19.27, per 1000 atoms: 0.58 Number of scatterers: 33424 At special positions: 0 Unit cell: (208.44, 157.68, 218.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 268 16.00 O 6352 8.00 N 5748 7.00 C 21056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, 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=2.00 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.06 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.05 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=2.05 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.04 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.02 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 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 E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 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-ASN " NAG E 1 " - " ASN A 141 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 200 " " NAG T 1 " - " ASN F 141 " " NAG U 1 " - " ASN G 141 " " NAG V 1 " - " ASN H 141 " " NAG W 1 " - " ASN I 262 " " NAG X 1 " - " ASN I 200 " " NAG Y 1 " - " ASN J 262 " " NAG Z 1 " - " ASN J 200 " " NAG a 1 " - " ASN K 262 " " NAG b 1 " - " ASN K 200 " Time building additional restraints: 8.87 Conformation dependent library (CDL) restraints added in 4.4 seconds 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7944 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 91 sheets defined 15.6% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.677A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.949A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.961A 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 11 removed outlier: 3.532A pdb=" N LYS B 10 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.534A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 401 removed outlier: 3.735A pdb=" N SER B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Proline residue: B 398 - end of helix removed outlier: 3.649A pdb=" N LEU B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.526A 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 41 removed outlier: 3.566A pdb=" N ASP C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.694A 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 Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.529A pdb=" N TYR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.972A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.741A 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 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.573A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.078A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.708A 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 Processing helix chain 'G' and resid 404 through 438 removed outlier: 3.558A pdb=" N ARG G 438 " --> pdb=" O ILE G 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.649A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.958A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 3.869A 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 202 through 206 removed outlier: 3.944A pdb=" N THR I 205 " --> pdb=" O THR I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 361 removed outlier: 3.601A pdb=" N VAL I 355 " --> pdb=" O PRO I 351 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN I 356 " --> pdb=" O HIS I 352 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 397 removed outlier: 4.125A pdb=" N SER I 368 " --> pdb=" O ALA I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 402 removed outlier: 3.829A pdb=" N THR I 402 " --> pdb=" O TYR I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 414 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.744A pdb=" N LYS J 10 " --> pdb=" O ASN J 7 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 7 through 12' Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.682A pdb=" N VAL J 355 " --> pdb=" O PRO J 351 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 397 removed outlier: 4.077A pdb=" N SER J 368 " --> pdb=" O ALA J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 401 Processing helix chain 'J' and resid 407 through 414 removed outlier: 3.801A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 350 through 361 removed outlier: 3.694A pdb=" N VAL K 355 " --> pdb=" O PRO K 351 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN K 356 " --> pdb=" O HIS K 352 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU K 361 " --> pdb=" O TYR K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 397 removed outlier: 4.104A pdb=" N SER K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 402 removed outlier: 3.537A pdb=" N LEU K 401 " --> pdb=" O PRO K 398 " (cutoff:3.500A) removed outlier: 3.722A 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 removed outlier: 3.507A pdb=" N ILE K 413 " --> pdb=" O TRP K 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 31 through 41 removed outlier: 3.853A pdb=" N ASP L 41 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.583A pdb=" N LEU L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.717A pdb=" N THR M 35 " --> pdb=" O ASN M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 56 removed outlier: 3.523A 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 Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 152 through 157 removed outlier: 3.597A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.911A pdb=" N SER O 179 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 4.126A 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: 3.551A pdb=" N LYS P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 5.335A pdb=" N SER P 179 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 3.703A 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 Processing helix chain 'Q' and resid 174 through 181 removed outlier: 4.896A pdb=" N SER Q 179 " --> pdb=" O HIS Q 176 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Q 181 " --> pdb=" O ARG Q 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.851A pdb=" N GLN A 160 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.933A pdb=" N MET A 31 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 135 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 33 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 131 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 129 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 127 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.448A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 127 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 129 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 131 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 33 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 135 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET A 31 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 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 296 through 305 removed outlier: 5.680A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 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 19 removed outlier: 3.543A pdb=" N CYS B 28 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 38 removed outlier: 10.057A pdb=" N SER B 51 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA B 70 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 66 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.299A pdb=" N HIS B 99 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ALA B 52 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N MET B 97 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ILE B 54 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLY B 95 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 15.890A pdb=" N ILE B 56 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 18.625A pdb=" N VAL B 93 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.169A pdb=" N GLU B 109 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB8, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.757A pdb=" N VAL B 227 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.961A pdb=" N GLU B 281 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 149 through 150 removed outlier: 6.566A pdb=" N PHE D 121 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR D 132 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 123 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 256 through 259 removed outlier: 3.549A pdb=" N THR D 244 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE D 207 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE D 223 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 256 through 259 removed outlier: 6.528A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AC6, first strand: chain 'F' and resid 15 through 19 removed outlier: 6.972A pdb=" N MET F 31 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL F 135 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL F 33 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 133 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA F 131 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER F 37 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 129 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA F 127 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA F 119 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 143 through 147 removed outlier: 6.524A pdb=" N ALA F 119 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA F 127 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 129 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER F 37 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA F 131 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 133 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL F 33 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL F 135 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET F 31 " --> pdb=" O VAL F 135 " (cutoff:3.500A) 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 51 through 54 Processing sheet with id=AD1, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD2, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD3, first strand: chain 'F' and resid 296 through 306 removed outlier: 5.783A pdb=" N ASP F 298 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS F 321 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 343 through 344 Processing sheet with id=AD5, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD6, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD7, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.460A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 140 through 147 removed outlier: 3.584A pdb=" N TYR G 137 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN G 142 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.618A pdb=" N TYR G 59 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AE2, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AE3, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AE4, first strand: chain 'G' and resid 297 through 306 removed outlier: 7.375A pdb=" N LEU G 299 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LYS G 321 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N CYS G 301 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR G 319 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL G 303 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR G 317 " --> pdb=" O VAL G 303 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR G 305 " --> pdb=" O VAL G 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AE6, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AE7, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AE8, first strand: chain 'H' and resid 15 through 19 removed outlier: 7.764A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 140 through 147 removed outlier: 6.499A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AF2, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AF3, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AF4, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AF5, first strand: chain 'H' and resid 296 through 306 removed outlier: 5.675A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 326 through 328 Processing sheet with id=AF7, first strand: chain 'H' and resid 330 through 332 Processing sheet with id=AF8, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AF9, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'I' and resid 37 through 38 removed outlier: 11.793A pdb=" N ILE I 54 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N ALA I 70 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE I 56 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.540A pdb=" N HIS I 99 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N ALA I 52 " --> pdb=" O MET I 97 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N MET I 97 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ILE I 54 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N GLY I 95 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 15.675A pdb=" N ILE I 56 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 18.620A pdb=" N VAL I 93 " --> pdb=" O ILE I 56 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 84 through 86 removed outlier: 4.141A pdb=" N GLU I 109 " --> pdb=" O TYR I 129 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 151 through 156 Processing sheet with id=AG5, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.644A pdb=" N VAL I 227 " --> pdb=" O ASP I 177 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AG7, first strand: chain 'I' and resid 274 through 277 Processing sheet with id=AG8, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG9, first strand: chain 'J' and resid 37 through 38 removed outlier: 16.700A pdb=" N GLN J 49 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N TYR J 69 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N SER J 51 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE J 67 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N GLN J 53 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N THR J 65 " --> pdb=" O GLN J 53 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY J 55 " --> pdb=" O ASP J 63 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.518A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 15.778A pdb=" N ILE J 56 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 18.828A pdb=" N VAL J 93 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AH3, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AH4, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AH5, first strand: chain 'J' and resid 167 through 169 Processing sheet with id=AH6, first strand: chain 'J' and resid 175 through 177 removed outlier: 3.502A pdb=" N THR J 175 " --> pdb=" O VAL J 229 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL J 227 " --> pdb=" O ASP J 177 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 181 through 183 Processing sheet with id=AH8, first strand: chain 'J' and resid 197 through 199 Processing sheet with id=AH9, first strand: chain 'J' and resid 274 through 278 removed outlier: 3.861A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AI2, first strand: chain 'K' and resid 46 through 54 removed outlier: 6.565A pdb=" N HIS K 99 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ALA K 52 " --> pdb=" O MET K 97 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N MET K 97 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ILE K 54 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N GLY K 95 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 66 through 69 Processing sheet with id=AI4, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.193A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 149 through 152 Processing sheet with id=AI6, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AI7, first strand: chain 'K' and resid 175 through 177 removed outlier: 3.690A pdb=" N THR K 175 " --> pdb=" O VAL K 229 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 229 " --> pdb=" O THR K 175 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL K 227 " --> pdb=" O ASP K 177 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 182 through 183 Processing sheet with id=AI9, first strand: chain 'K' and resid 198 through 199 removed outlier: 3.643A 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 278 removed outlier: 3.731A pdb=" N GLU K 281 " --> pdb=" O GLY K 278 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 149 through 150 removed outlier: 3.863A pdb=" N GLY O 131 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS O 125 " --> pdb=" O VAL O 129 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL O 129 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR O 132 " --> pdb=" O PRO O 143 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 256 through 259 removed outlier: 4.936A pdb=" N PHE O 207 " --> pdb=" O LEU O 246 " (cutoff:3.500A) removed outlier: 6.847A 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: 6.593A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 7.909A 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: 4.205A pdb=" N GLY P 131 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS P 125 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL P 129 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N TYR P 132 " --> pdb=" O PRO P 143 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS P 134 " --> pdb=" O MET P 141 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'P' and resid 256 through 259 removed outlier: 4.979A pdb=" N PHE P 207 " --> pdb=" O LEU P 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA P 232 " --> pdb=" O ILE P 223 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY P 237 " --> pdb=" O GLU P 265 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'P' and resid 256 through 259 removed outlier: 6.021A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY P 237 " --> pdb=" O GLU P 265 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 149 through 150 removed outlier: 6.406A pdb=" N PHE Q 121 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR Q 132 " --> pdb=" O PHE Q 121 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL Q 123 " --> pdb=" O THR Q 130 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N TYR Q 132 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Q' and resid 256 through 259 removed outlier: 3.528A pdb=" N THR Q 244 " --> pdb=" O ILE Q 209 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE Q 207 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 6.952A 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: 6.391A pdb=" N VAL Q 249 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL Q 234 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TRP Q 251 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA Q 232 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3216 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: 13.06 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7874 1.33 - 1.46: 9260 1.46 - 1.58: 16793 1.58 - 1.71: 1 1.71 - 1.84: 364 Bond restraints: 34292 Sorted by residual: bond pdb=" CG1 ILE J 115 " pdb=" CD1 ILE J 115 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.54e+00 bond pdb=" CA CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.64e-02 3.72e+03 6.04e+00 bond pdb=" CA TYR B 9 " pdb=" C TYR B 9 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.80e-02 3.09e+03 5.77e+00 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.566 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 BMA b 3 " pdb=" C2 BMA b 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 34287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 45594 2.71 - 5.41: 982 5.41 - 8.12: 97 8.12 - 10.83: 18 10.83 - 13.54: 13 Bond angle restraints: 46704 Sorted by residual: angle pdb=" C LYS K 104 " pdb=" N CYS K 105 " pdb=" CA CYS K 105 " ideal model delta sigma weight residual 122.90 109.36 13.54 2.07e+00 2.33e-01 4.28e+01 angle pdb=" C THR H 249 " pdb=" CA THR H 249 " pdb=" CB THR H 249 " ideal model delta sigma weight residual 115.79 108.55 7.24 1.19e+00 7.06e-01 3.70e+01 angle pdb=" C PHE K 50 " pdb=" CA PHE K 50 " pdb=" CB PHE K 50 " ideal model delta sigma weight residual 112.99 100.27 12.72 2.10e+00 2.27e-01 3.67e+01 angle pdb=" CA PRO I 363 " pdb=" N PRO I 363 " pdb=" CD PRO I 363 " ideal model delta sigma weight residual 112.00 103.84 8.16 1.40e+00 5.10e-01 3.40e+01 angle pdb=" C THR A 249 " pdb=" CA THR A 249 " pdb=" CB THR A 249 " ideal model delta sigma weight residual 115.79 108.95 6.84 1.19e+00 7.06e-01 3.30e+01 ... (remaining 46699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 19890 23.05 - 46.10: 956 46.10 - 69.15: 101 69.15 - 92.20: 91 92.20 - 115.25: 46 Dihedral angle restraints: 21084 sinusoidal: 8692 harmonic: 12392 Sorted by residual: dihedral pdb=" CB CYS A 306 " pdb=" SG CYS A 306 " pdb=" SG CYS A 380 " pdb=" CB CYS A 380 " ideal model delta sinusoidal sigma weight residual -86.00 -0.89 -85.11 1 1.00e+01 1.00e-02 8.78e+01 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 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA VAL A 140 " pdb=" C VAL A 140 " pdb=" N ASN A 141 " pdb=" CA ASN A 141 " ideal model delta harmonic sigma weight residual 180.00 143.01 36.99 0 5.00e+00 4.00e-02 5.47e+01 ... (remaining 21081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 5270 0.216 - 0.432: 24 0.432 - 0.648: 1 0.648 - 0.863: 0 0.863 - 1.079: 1 Chirality restraints: 5296 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN J 262 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5293 not shown) Planarity restraints: 6004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 141 " 0.008 2.00e-02 2.50e+03 6.32e-02 4.99e+01 pdb=" CG ASN A 141 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 141 " 0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 141 " -0.084 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 50 " 0.052 2.00e-02 2.50e+03 4.04e-02 2.85e+01 pdb=" CG PHE K 50 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE K 50 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE K 50 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE K 50 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 21 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO H 22 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 22 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO H 22 " -0.064 5.00e-02 4.00e+02 ... (remaining 6001 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 326 2.63 - 3.20: 28708 3.20 - 3.76: 47306 3.76 - 4.33: 65128 4.33 - 4.90: 112885 Nonbonded interactions: 254353 Sorted by model distance: nonbonded pdb=" OH TYR K 69 " pdb=" OD1 ASP K 117 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OE1 GLN B 224 " model vdw 2.126 3.040 nonbonded pdb=" OG SER J 59 " pdb=" OD1 ASN J 61 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLU J 166 " pdb=" OH TYR M 49 " model vdw 2.162 3.040 nonbonded pdb=" NZ LYS O 188 " pdb=" OG1 THR O 250 " model vdw 2.171 3.120 ... (remaining 254348 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 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 75.350 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 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 : 0.008 0.114 34384 Z= 0.338 Angle : 0.972 18.498 46924 Z= 0.499 Chirality : 0.059 1.079 5296 Planarity : 0.007 0.173 5992 Dihedral : 15.115 115.249 12972 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.95 % Favored : 92.81 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.25 (0.12), residues: 4244 helix: 1.68 (0.22), residues: 564 sheet: -0.72 (0.14), residues: 1296 loop : -1.55 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 195 HIS 0.018 0.003 HIS A 230 PHE 0.091 0.003 PHE K 50 TYR 0.040 0.003 TYR B 305 ARG 0.013 0.001 ARG H 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 12) link_NAG-ASN : angle 5.18391 ( 36) link_BETA1-4 : bond 0.01245 ( 24) link_BETA1-4 : angle 2.86705 ( 72) hydrogen bonds : bond 0.14420 ( 1182) hydrogen bonds : angle 6.89039 ( 3216) SS BOND : bond 0.00871 ( 56) SS BOND : angle 2.32267 ( 112) covalent geometry : bond 0.00837 (34292) covalent geometry : angle 0.95025 (46704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 957 time to evaluate : 3.346 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: A 101 THR cc_start: 0.5945 (p) cc_final: 0.5649 (p) REVERT: B 12 THR cc_start: 0.4998 (p) cc_final: 0.4705 (p) REVERT: D 111 MET cc_start: 0.7386 (ptt) cc_final: 0.7163 (ptt) REVERT: D 120 ILE cc_start: 0.8391 (mt) cc_final: 0.8137 (tt) REVERT: D 193 TYR cc_start: 0.6927 (m-80) cc_final: 0.6591 (m-80) REVERT: D 201 GLN cc_start: 0.7281 (mt0) cc_final: 0.6864 (mt0) REVERT: D 207 PHE cc_start: 0.6943 (m-80) cc_final: 0.6687 (m-80) REVERT: D 221 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: F 289 ARG cc_start: 0.6866 (mmt180) cc_final: 0.6615 (mtp85) REVERT: G 402 MET cc_start: 0.5185 (ttp) cc_final: 0.4974 (tpt) REVERT: H 287 PHE cc_start: 0.6822 (m-80) cc_final: 0.6542 (m-80) REVERT: H 402 MET cc_start: 0.6786 (mmt) cc_final: 0.6186 (mmt) REVERT: I 199 TYR cc_start: 0.5964 (p90) cc_final: 0.5750 (p90) REVERT: I 210 THR cc_start: 0.8177 (p) cc_final: 0.7903 (m) REVERT: I 340 GLN cc_start: 0.4184 (tt0) cc_final: 0.3514 (tt0) REVERT: K 199 TYR cc_start: 0.5235 (p90) cc_final: 0.5013 (p90) REVERT: L 45 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7539 (mtt-85) REVERT: M 49 TYR cc_start: 0.5888 (m-80) cc_final: 0.5623 (m-80) REVERT: O 140 VAL cc_start: 0.6918 (t) cc_final: 0.6617 (t) REVERT: O 177 MET cc_start: 0.8294 (mtp) cc_final: 0.7949 (mtt) REVERT: O 183 LYS cc_start: 0.6887 (tppp) cc_final: 0.6648 (mtmt) REVERT: O 258 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6895 (ttp80) REVERT: P 184 TYR cc_start: 0.6320 (p90) cc_final: 0.5872 (p90) REVERT: Q 113 MET cc_start: 0.7416 (tpt) cc_final: 0.6874 (tpt) REVERT: Q 114 LYS cc_start: 0.6828 (pttm) cc_final: 0.6472 (ptpt) REVERT: Q 139 LYS cc_start: 0.3356 (pttm) cc_final: 0.3040 (mtpp) outliers start: 1 outliers final: 0 residues processed: 958 average time/residue: 0.4637 time to fit residues: 698.9146 Evaluate side-chains 560 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 329 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 245 optimal weight: 0.9990 chunk 381 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS B 236 GLN B 340 GLN D 176 HIS D 186 HIS ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN H 216 ASN I 170 HIS I 255 HIS I 352 HIS ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 HIS J 340 GLN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS K 236 GLN K 255 HIS M 42 ASN N 20 GLN ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135496 restraints weight = 41424.198| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.53 r_work: 0.3388 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34384 Z= 0.158 Angle : 0.743 11.938 46924 Z= 0.369 Chirality : 0.048 0.304 5296 Planarity : 0.005 0.075 5992 Dihedral : 9.261 66.027 5364 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.85 % Favored : 94.93 % Rotamer: Outliers : 3.01 % Allowed : 10.55 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.88 (0.13), residues: 4244 helix: 2.20 (0.23), residues: 536 sheet: -0.21 (0.14), residues: 1164 loop : -1.45 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 329 HIS 0.008 0.001 HIS D 125 PHE 0.038 0.002 PHE K 50 TYR 0.026 0.002 TYR J 18 ARG 0.009 0.001 ARG J 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 12) link_NAG-ASN : angle 3.48832 ( 36) link_BETA1-4 : bond 0.00905 ( 24) link_BETA1-4 : angle 3.42806 ( 72) hydrogen bonds : bond 0.03798 ( 1182) hydrogen bonds : angle 5.45804 ( 3216) SS BOND : bond 0.00445 ( 56) SS BOND : angle 1.21635 ( 112) covalent geometry : bond 0.00360 (34292) covalent geometry : angle 0.72389 (46704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 658 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.6444 (mp0) cc_final: 0.6073 (mt-10) REVERT: A 177 ILE cc_start: 0.7474 (pt) cc_final: 0.7000 (pt) REVERT: A 202 ASP cc_start: 0.7151 (p0) cc_final: 0.6583 (p0) REVERT: A 209 GLU cc_start: 0.7160 (tp30) cc_final: 0.6952 (mm-30) REVERT: D 221 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7240 (mtp85) REVERT: D 252 ASN cc_start: 0.7343 (m-40) cc_final: 0.7090 (m110) REVERT: F 354 LEU cc_start: 0.7311 (mt) cc_final: 0.7050 (mt) REVERT: G 402 MET cc_start: 0.5687 (ttp) cc_final: 0.5197 (tpt) REVERT: H 75 ASP cc_start: 0.5965 (t70) cc_final: 0.5633 (t0) REVERT: H 77 GLN cc_start: 0.6242 (mm-40) cc_final: 0.5768 (mm-40) REVERT: H 99 GLU cc_start: 0.7016 (mp0) cc_final: 0.6476 (tp30) REVERT: H 151 ASP cc_start: 0.5975 (t70) cc_final: 0.5657 (t70) REVERT: H 291 VAL cc_start: 0.7930 (t) cc_final: 0.7707 (t) REVERT: H 402 MET cc_start: 0.6884 (mmt) cc_final: 0.6413 (mmt) REVERT: I 210 THR cc_start: 0.8245 (p) cc_final: 0.8009 (m) REVERT: I 223 GLU cc_start: 0.7906 (pm20) cc_final: 0.7673 (pm20) REVERT: I 282 VAL cc_start: 0.6753 (t) cc_final: 0.6416 (t) REVERT: K 97 MET cc_start: 0.4679 (OUTLIER) cc_final: 0.4211 (tpt) REVERT: K 215 MET cc_start: 0.6966 (mmt) cc_final: 0.6574 (mmt) REVERT: K 344 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: L 45 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7772 (mtt-85) REVERT: L 50 ASP cc_start: 0.7566 (m-30) cc_final: 0.6517 (p0) REVERT: O 111 MET cc_start: 0.6974 (pmm) cc_final: 0.6693 (pmm) REVERT: O 183 LYS cc_start: 0.6833 (tppp) cc_final: 0.6620 (mtpt) REVERT: P 184 TYR cc_start: 0.6019 (p90) cc_final: 0.5722 (p90) REVERT: Q 113 MET cc_start: 0.7521 (tpt) cc_final: 0.7032 (tpt) REVERT: Q 114 LYS cc_start: 0.7036 (pttm) cc_final: 0.6717 (ptpt) REVERT: Q 253 LYS cc_start: 0.7747 (tptp) cc_final: 0.7305 (tppt) outliers start: 109 outliers final: 60 residues processed: 732 average time/residue: 0.4148 time to fit residues: 500.8526 Evaluate side-chains 577 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 515 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 170 HIS Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 329 TRP Chi-restraints excluded: chain K residue 333 ASP Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 94 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 chunk 328 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 49 GLN B 62 HIS B 131 HIS B 232 HIS D 197 HIS F 275 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN G 187 GLN H 18 HIS H 331 HIS I 53 GLN I 61 ASN I 232 HIS I 340 GLN J 131 HIS ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 HIS ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS M 42 ASN M 53 GLN O 252 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.184035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135384 restraints weight = 41600.610| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.51 r_work: 0.3368 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 34384 Z= 0.164 Angle : 0.704 11.961 46924 Z= 0.351 Chirality : 0.046 0.334 5296 Planarity : 0.005 0.066 5992 Dihedral : 6.600 56.325 5364 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.39 % Rotamer: Outliers : 3.40 % Allowed : 13.23 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.77 (0.13), residues: 4244 helix: 2.17 (0.23), residues: 560 sheet: -0.34 (0.14), residues: 1252 loop : -1.29 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 195 HIS 0.071 0.002 HIS D 186 PHE 0.037 0.002 PHE K 50 TYR 0.032 0.002 TYR A 93 ARG 0.008 0.001 ARG K 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 12) link_NAG-ASN : angle 3.00362 ( 36) link_BETA1-4 : bond 0.00954 ( 24) link_BETA1-4 : angle 2.51440 ( 72) hydrogen bonds : bond 0.03695 ( 1182) hydrogen bonds : angle 5.01674 ( 3216) SS BOND : bond 0.00772 ( 56) SS BOND : angle 1.69507 ( 112) covalent geometry : bond 0.00374 (34292) covalent geometry : angle 0.68856 (46704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 582 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7317 (tp30) cc_final: 0.7100 (mm-30) REVERT: B 67 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7659 (mt) REVERT: B 232 HIS cc_start: 0.4349 (OUTLIER) cc_final: 0.4002 (t-170) REVERT: D 221 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7278 (mtp85) REVERT: F 67 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: F 220 LYS cc_start: 0.8401 (ptmt) cc_final: 0.8194 (ttpt) REVERT: G 402 MET cc_start: 0.6099 (ttp) cc_final: 0.5718 (tpt) REVERT: H 99 GLU cc_start: 0.7488 (mp0) cc_final: 0.6851 (tp30) REVERT: H 151 ASP cc_start: 0.6688 (t70) cc_final: 0.6336 (t70) REVERT: H 269 MET cc_start: 0.7522 (mtm) cc_final: 0.7283 (mtm) REVERT: H 402 MET cc_start: 0.7087 (mmt) cc_final: 0.6694 (mmt) REVERT: I 168 ASP cc_start: 0.7894 (m-30) cc_final: 0.7603 (m-30) REVERT: I 199 TYR cc_start: 0.5624 (p90) cc_final: 0.5376 (p90) REVERT: I 282 VAL cc_start: 0.7427 (t) cc_final: 0.7127 (t) REVERT: I 361 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5578 (pt) REVERT: J 250 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7417 (ttm-80) REVERT: J 361 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.4366 (pt) REVERT: K 97 MET cc_start: 0.5658 (tpt) cc_final: 0.5328 (tpt) REVERT: K 215 MET cc_start: 0.7197 (mmt) cc_final: 0.6905 (mmp) REVERT: K 329 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.7391 (t-100) REVERT: L 50 ASP cc_start: 0.7622 (m-30) cc_final: 0.6626 (p0) REVERT: N 8 MET cc_start: 0.5818 (pmm) cc_final: 0.5172 (pmm) REVERT: O 183 LYS cc_start: 0.6951 (tppp) cc_final: 0.6740 (mtpt) REVERT: Q 111 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.5458 (ptp) REVERT: Q 113 MET cc_start: 0.7557 (tpt) cc_final: 0.7029 (tpt) REVERT: Q 253 LYS cc_start: 0.7739 (tptp) cc_final: 0.7309 (tppt) outliers start: 123 outliers final: 71 residues processed: 664 average time/residue: 0.4364 time to fit residues: 480.5137 Evaluate side-chains 548 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 470 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 251 LYS Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 329 TRP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 170 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 98 optimal weight: 40.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 112 GLN B 255 HIS D 197 HIS F 160 GLN F 264 ASN F 394 HIS G 340 GLN H 252 ASN I 348 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 HIS J 340 GLN J 348 HIS K 53 GLN K 62 HIS K 134 GLN K 226 HIS K 277 HIS K 331 ASN M 42 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115266 restraints weight = 40768.228| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.05 r_work: 0.3224 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.8235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 34384 Z= 0.230 Angle : 0.844 18.119 46924 Z= 0.425 Chirality : 0.052 0.798 5296 Planarity : 0.006 0.067 5992 Dihedral : 6.364 58.930 5364 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.03 % Favored : 93.73 % Rotamer: Outliers : 4.72 % Allowed : 14.56 % Favored : 80.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.17 % 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: -0.98 (0.13), residues: 4244 helix: 2.29 (0.23), residues: 512 sheet: -0.39 (0.14), residues: 1292 loop : -1.50 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 329 HIS 0.081 0.002 HIS B 232 PHE 0.053 0.002 PHE K 50 TYR 0.028 0.002 TYR F 93 ARG 0.014 0.001 ARG J 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 12) link_NAG-ASN : angle 4.65937 ( 36) link_BETA1-4 : bond 0.00909 ( 24) link_BETA1-4 : angle 2.64682 ( 72) hydrogen bonds : bond 0.04235 ( 1182) hydrogen bonds : angle 5.15169 ( 3216) SS BOND : bond 0.00782 ( 56) SS BOND : angle 2.67782 ( 112) covalent geometry : bond 0.00546 (34292) covalent geometry : angle 0.81931 (46704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 514 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: B 174 ASP cc_start: 0.8091 (p0) cc_final: 0.7724 (p0) REVERT: B 260 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8911 (mp) REVERT: B 276 ILE cc_start: 0.8735 (mt) cc_final: 0.8452 (mp) REVERT: C 8 MET cc_start: 0.6745 (mpp) cc_final: 0.6317 (mpp) REVERT: D 221 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7407 (mtp180) REVERT: D 252 ASN cc_start: 0.7826 (m-40) cc_final: 0.7132 (m-40) REVERT: F 18 HIS cc_start: 0.9086 (OUTLIER) cc_final: 0.8690 (t-170) REVERT: F 38 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8501 (tt) REVERT: F 61 LYS cc_start: 0.6864 (tttp) cc_final: 0.6428 (tttp) REVERT: F 93 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5407 (p90) REVERT: F 220 LYS cc_start: 0.8883 (ptmt) cc_final: 0.8625 (ttpt) REVERT: G 246 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: G 341 GLU cc_start: 0.8344 (pm20) cc_final: 0.8012 (pm20) REVERT: G 362 SER cc_start: 0.8921 (t) cc_final: 0.8522 (m) REVERT: G 402 MET cc_start: 0.6767 (ttp) cc_final: 0.6098 (tpt) REVERT: H 19 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7304 (mt) REVERT: H 79 LYS cc_start: 0.8374 (tttm) cc_final: 0.8023 (ttmm) REVERT: I 84 LYS cc_start: 0.8431 (mtpp) cc_final: 0.8020 (mttp) REVERT: I 199 TYR cc_start: 0.6031 (p90) cc_final: 0.5324 (p90) REVERT: I 325 MET cc_start: 0.9117 (tmm) cc_final: 0.8810 (tmm) REVERT: J 53 GLN cc_start: 0.8262 (mt0) cc_final: 0.7768 (mt0) REVERT: J 71 ASP cc_start: 0.7773 (t0) cc_final: 0.7391 (p0) REVERT: J 97 MET cc_start: 0.8358 (tpp) cc_final: 0.7810 (tpt) REVERT: K 53 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7155 (mp-120) REVERT: K 75 ILE cc_start: 0.8304 (pt) cc_final: 0.7972 (mt) REVERT: K 83 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7370 (pt) REVERT: K 134 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7402 (mm-40) REVERT: K 215 MET cc_start: 0.7247 (mmt) cc_final: 0.6975 (mmt) REVERT: K 299 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7587 (pp) REVERT: K 302 ASP cc_start: 0.8860 (t0) cc_final: 0.8645 (t0) REVERT: N 8 MET cc_start: 0.6217 (pmm) cc_final: 0.5573 (pmm) REVERT: P 227 LYS cc_start: 0.7274 (mmtm) cc_final: 0.6562 (mtpp) REVERT: Q 113 MET cc_start: 0.7466 (tpt) cc_final: 0.6829 (tpt) REVERT: Q 253 LYS cc_start: 0.7825 (tptp) cc_final: 0.7442 (tppt) REVERT: Q 255 MET cc_start: 0.5908 (mmt) cc_final: 0.5423 (mmt) outliers start: 171 outliers final: 92 residues processed: 635 average time/residue: 0.4080 time to fit residues: 426.2957 Evaluate side-chains 523 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 420 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 170 HIS Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 134 GLN Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 185 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 400 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 281 ASN B 49 GLN B 62 HIS B 112 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS F 118 HIS F 411 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN I 184 GLN J 77 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS K 285 HIS M 42 ASN O 252 ASN Q 197 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103291 restraints weight = 40853.713| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.15 r_work: 0.3053 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.9734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 34384 Z= 0.307 Angle : 0.854 18.109 46924 Z= 0.430 Chirality : 0.053 0.307 5296 Planarity : 0.006 0.071 5992 Dihedral : 6.550 59.614 5364 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.41 % Favored : 93.40 % Rotamer: Outliers : 5.41 % Allowed : 15.58 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4244 helix: 2.07 (0.23), residues: 512 sheet: -0.63 (0.14), residues: 1232 loop : -1.61 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 235 HIS 0.027 0.002 HIS B 232 PHE 0.046 0.003 PHE K 50 TYR 0.033 0.003 TYR F 93 ARG 0.010 0.001 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.01622 ( 12) link_NAG-ASN : angle 4.77703 ( 36) link_BETA1-4 : bond 0.01122 ( 24) link_BETA1-4 : angle 2.65304 ( 72) hydrogen bonds : bond 0.04734 ( 1182) hydrogen bonds : angle 5.26842 ( 3216) SS BOND : bond 0.00577 ( 56) SS BOND : angle 2.24180 ( 112) covalent geometry : bond 0.00784 (34292) covalent geometry : angle 0.83180 (46704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 453 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.7569 (p0) cc_final: 0.7359 (p0) REVERT: A 300 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8739 (m) REVERT: B 46 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8695 (mp) REVERT: B 101 ILE cc_start: 0.8682 (tt) cc_final: 0.8325 (mt) REVERT: B 165 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: B 196 LYS cc_start: 0.7460 (ptmm) cc_final: 0.7170 (pttm) REVERT: B 224 GLN cc_start: 0.8124 (mt0) cc_final: 0.7903 (mt0) REVERT: B 251 LYS cc_start: 0.7393 (mmtm) cc_final: 0.6945 (mtpp) REVERT: B 284 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 289 ASP cc_start: 0.8514 (t0) cc_final: 0.8285 (t0) REVERT: D 113 MET cc_start: 0.8160 (mmm) cc_final: 0.7437 (mmm) REVERT: F 93 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5556 (p90) REVERT: F 117 ASP cc_start: 0.8440 (m-30) cc_final: 0.8000 (t0) REVERT: F 347 LYS cc_start: 0.7216 (mtmm) cc_final: 0.6879 (mttm) REVERT: F 384 LYS cc_start: 0.6022 (ttpt) cc_final: 0.5721 (ttpt) REVERT: G 362 SER cc_start: 0.8993 (t) cc_final: 0.8699 (m) REVERT: G 402 MET cc_start: 0.7381 (ttp) cc_final: 0.6761 (tpt) REVERT: H 79 LYS cc_start: 0.8496 (tttm) cc_final: 0.8169 (ttmm) REVERT: H 230 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8495 (p-80) REVERT: H 339 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9238 (mp) REVERT: H 340 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: I 199 TYR cc_start: 0.6292 (p90) cc_final: 0.5862 (p90) REVERT: I 223 GLU cc_start: 0.8233 (pm20) cc_final: 0.7957 (pm20) REVERT: I 224 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6311 (mt0) REVERT: I 251 LYS cc_start: 0.8210 (mptt) cc_final: 0.7476 (mtpp) REVERT: I 304 GLN cc_start: 0.8581 (tt0) cc_final: 0.8367 (mt0) REVERT: J 212 ASN cc_start: 0.7972 (p0) cc_final: 0.7694 (p0) REVERT: J 231 ASP cc_start: 0.7662 (t0) cc_final: 0.7398 (t0) REVERT: K 272 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: K 301 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8616 (tt0) REVERT: K 302 ASP cc_start: 0.9014 (t0) cc_final: 0.8806 (t0) REVERT: N 8 MET cc_start: 0.6075 (pmm) cc_final: 0.5384 (pmm) REVERT: O 162 LYS cc_start: 0.7393 (tmtt) cc_final: 0.7051 (mtpt) REVERT: O 253 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8277 (tptt) REVERT: Q 111 MET cc_start: 0.6268 (ppp) cc_final: 0.5776 (mmm) REVERT: Q 113 MET cc_start: 0.7533 (tpt) cc_final: 0.6959 (tpt) REVERT: Q 253 LYS cc_start: 0.7828 (tptp) cc_final: 0.7479 (tppt) REVERT: Q 255 MET cc_start: 0.5993 (mmt) cc_final: 0.5151 (mmt) outliers start: 196 outliers final: 127 residues processed: 603 average time/residue: 0.4408 time to fit residues: 444.0432 Evaluate side-chains 531 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 394 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 298 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 19 optimal weight: 0.0870 chunk 348 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 411 GLN G 3 HIS ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 175 ASN I 184 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 HIS K 226 HIS K 255 HIS M 42 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123210 restraints weight = 40608.189| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.20 r_work: 0.3198 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.9854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34384 Z= 0.115 Angle : 0.631 11.906 46924 Z= 0.317 Chirality : 0.045 0.290 5296 Planarity : 0.005 0.061 5992 Dihedral : 5.910 57.503 5364 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 3.56 % Allowed : 18.18 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.91 (0.13), residues: 4244 helix: 2.62 (0.23), residues: 512 sheet: -0.46 (0.14), residues: 1224 loop : -1.42 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 170 HIS 0.006 0.001 HIS D 186 PHE 0.022 0.001 PHE K 50 TYR 0.020 0.001 TYR I 359 ARG 0.005 0.000 ARG J 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 12) link_NAG-ASN : angle 3.44401 ( 36) link_BETA1-4 : bond 0.00885 ( 24) link_BETA1-4 : angle 2.32767 ( 72) hydrogen bonds : bond 0.03512 ( 1182) hydrogen bonds : angle 4.85535 ( 3216) SS BOND : bond 0.00369 ( 56) SS BOND : angle 1.56821 ( 112) covalent geometry : bond 0.00259 (34292) covalent geometry : angle 0.61404 (46704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 436 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.7548 (p0) cc_final: 0.7338 (p0) REVERT: A 300 THR cc_start: 0.9012 (m) cc_final: 0.8808 (m) REVERT: B 165 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: B 196 LYS cc_start: 0.7605 (ptmm) cc_final: 0.7354 (pttm) REVERT: B 251 LYS cc_start: 0.7402 (mmtm) cc_final: 0.7051 (mtpp) REVERT: D 113 MET cc_start: 0.8395 (mmm) cc_final: 0.7646 (mmm) REVERT: D 114 LYS cc_start: 0.8110 (ptmt) cc_final: 0.7867 (ptmm) REVERT: D 252 ASN cc_start: 0.8000 (m-40) cc_final: 0.7566 (m110) REVERT: F 29 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8955 (mp) REVERT: F 117 ASP cc_start: 0.8457 (m-30) cc_final: 0.8218 (t0) REVERT: F 347 LYS cc_start: 0.7415 (mtmm) cc_final: 0.7116 (mttm) REVERT: G 320 TYR cc_start: 0.8799 (p90) cc_final: 0.8470 (p90) REVERT: G 327 ASP cc_start: 0.8376 (p0) cc_final: 0.8139 (p0) REVERT: G 362 SER cc_start: 0.9107 (t) cc_final: 0.8843 (m) REVERT: G 402 MET cc_start: 0.7436 (ttp) cc_final: 0.6886 (tpt) REVERT: H 31 MET cc_start: 0.8914 (mtm) cc_final: 0.8648 (mtm) REVERT: H 79 LYS cc_start: 0.8467 (tttm) cc_final: 0.8230 (ttmm) REVERT: H 230 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.8255 (p-80) REVERT: H 339 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9243 (mp) REVERT: H 402 MET cc_start: 0.7528 (mmt) cc_final: 0.6967 (mmt) REVERT: I 199 TYR cc_start: 0.6335 (p90) cc_final: 0.5904 (p90) REVERT: I 223 GLU cc_start: 0.8214 (pm20) cc_final: 0.7999 (pm20) REVERT: I 224 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6397 (mt0) REVERT: I 251 LYS cc_start: 0.7972 (mptt) cc_final: 0.7320 (mtpp) REVERT: J 97 MET cc_start: 0.8786 (tpp) cc_final: 0.8487 (tpt) REVERT: J 212 ASN cc_start: 0.8056 (p0) cc_final: 0.7719 (p0) REVERT: K 272 GLU cc_start: 0.8907 (pm20) cc_final: 0.8623 (mp0) REVERT: K 301 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8732 (tt0) REVERT: L 50 ASP cc_start: 0.8180 (m-30) cc_final: 0.7948 (m-30) REVERT: N 8 MET cc_start: 0.6118 (pmm) cc_final: 0.5410 (pmm) REVERT: O 253 LYS cc_start: 0.8736 (tmmt) cc_final: 0.8227 (tptt) REVERT: P 227 LYS cc_start: 0.7520 (mmtm) cc_final: 0.6990 (mtpp) REVERT: Q 111 MET cc_start: 0.6297 (ppp) cc_final: 0.5667 (mmm) REVERT: Q 113 MET cc_start: 0.7611 (tpt) cc_final: 0.7376 (tpt) REVERT: Q 253 LYS cc_start: 0.7910 (tptp) cc_final: 0.7585 (tppt) outliers start: 129 outliers final: 91 residues processed: 525 average time/residue: 0.4131 time to fit residues: 358.7715 Evaluate side-chains 491 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 395 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 182 ASP Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 140 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 254 optimal weight: 0.6980 chunk 394 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 31 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 232 HIS D 196 HIS F 411 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 175 ASN I 331 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS L 53 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118465 restraints weight = 40635.346| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.23 r_work: 0.3088 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 1.0217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 34384 Z= 0.192 Angle : 0.716 12.418 46924 Z= 0.358 Chirality : 0.047 0.277 5296 Planarity : 0.005 0.062 5992 Dihedral : 5.994 57.429 5364 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 4.17 % Allowed : 18.34 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.96 (0.13), residues: 4244 helix: 2.69 (0.23), residues: 512 sheet: -0.51 (0.14), residues: 1232 loop : -1.47 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 235 HIS 0.009 0.001 HIS B 287 PHE 0.044 0.002 PHE K 50 TYR 0.030 0.002 TYR F 93 ARG 0.006 0.000 ARG J 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 12) link_NAG-ASN : angle 3.62468 ( 36) link_BETA1-4 : bond 0.00886 ( 24) link_BETA1-4 : angle 2.40587 ( 72) hydrogen bonds : bond 0.03944 ( 1182) hydrogen bonds : angle 4.92683 ( 3216) SS BOND : bond 0.00357 ( 56) SS BOND : angle 2.08067 ( 112) covalent geometry : bond 0.00482 (34292) covalent geometry : angle 0.69696 (46704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 419 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.7825 (p0) cc_final: 0.7582 (p0) REVERT: B 163 THR cc_start: 0.7959 (m) cc_final: 0.7002 (m) REVERT: B 165 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: B 196 LYS cc_start: 0.7702 (ptmm) cc_final: 0.7467 (pttm) REVERT: B 250 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: B 251 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7466 (mtpp) REVERT: B 387 MET cc_start: 0.7212 (mtt) cc_final: 0.6934 (mtp) REVERT: D 113 MET cc_start: 0.8333 (mmm) cc_final: 0.7671 (mmm) REVERT: D 114 LYS cc_start: 0.8127 (ptmt) cc_final: 0.7896 (ptmm) REVERT: D 141 MET cc_start: 0.8400 (ptp) cc_final: 0.8152 (ptp) REVERT: F 29 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8935 (mp) REVERT: F 130 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8136 (ptmt) REVERT: F 347 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7250 (mttm) REVERT: G 162 ILE cc_start: 0.8191 (mm) cc_final: 0.7878 (mm) REVERT: G 362 SER cc_start: 0.9085 (t) cc_final: 0.8868 (m) REVERT: G 402 MET cc_start: 0.7583 (ttp) cc_final: 0.6942 (tpt) REVERT: H 79 LYS cc_start: 0.8611 (tttm) cc_final: 0.8346 (ttmm) REVERT: H 84 VAL cc_start: 0.9305 (t) cc_final: 0.8891 (m) REVERT: H 339 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9218 (mp) REVERT: H 340 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: H 402 MET cc_start: 0.7573 (mmt) cc_final: 0.6964 (mmt) REVERT: I 53 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: I 199 TYR cc_start: 0.6256 (p90) cc_final: 0.5875 (p90) REVERT: I 223 GLU cc_start: 0.8265 (pm20) cc_final: 0.8042 (pm20) REVERT: I 224 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6443 (mt0) REVERT: I 251 LYS cc_start: 0.8217 (mptt) cc_final: 0.7505 (mtpp) REVERT: J 97 MET cc_start: 0.8863 (tpp) cc_final: 0.8603 (tpt) REVERT: J 196 LYS cc_start: 0.7187 (mtmt) cc_final: 0.6573 (mtpp) REVERT: J 231 ASP cc_start: 0.7543 (t0) cc_final: 0.7235 (t0) REVERT: J 354 ILE cc_start: 0.8177 (mm) cc_final: 0.7941 (mt) REVERT: K 50 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: K 272 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: K 301 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8706 (tt0) REVERT: L 50 ASP cc_start: 0.8236 (m-30) cc_final: 0.8027 (m-30) REVERT: N 8 MET cc_start: 0.6239 (pmm) cc_final: 0.5531 (pmm) REVERT: O 253 LYS cc_start: 0.8811 (tmmt) cc_final: 0.8330 (tptt) REVERT: P 227 LYS cc_start: 0.7600 (mmtm) cc_final: 0.6987 (mtpp) REVERT: Q 253 LYS cc_start: 0.7915 (tptp) cc_final: 0.7591 (tppt) outliers start: 151 outliers final: 103 residues processed: 524 average time/residue: 0.4142 time to fit residues: 352.4904 Evaluate side-chains 509 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 397 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 256 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 chunk 349 optimal weight: 0.5980 chunk 268 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 chunk 188 optimal weight: 0.0030 chunk 294 optimal weight: 0.9980 chunk 318 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN B 232 HIS F 411 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 175 ASN I 120 ASN J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS L 53 GLN M 42 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122338 restraints weight = 40452.926| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.22 r_work: 0.3173 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 1.0286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34384 Z= 0.104 Angle : 0.602 10.715 46924 Z= 0.301 Chirality : 0.044 0.250 5296 Planarity : 0.004 0.060 5992 Dihedral : 5.655 58.118 5364 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 3.29 % Allowed : 19.48 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.74 (0.13), residues: 4244 helix: 2.90 (0.23), residues: 512 sheet: -0.36 (0.14), residues: 1280 loop : -1.36 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 329 HIS 0.006 0.001 HIS H 230 PHE 0.025 0.001 PHE K 50 TYR 0.024 0.001 TYR I 359 ARG 0.007 0.000 ARG J 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 12) link_NAG-ASN : angle 3.02984 ( 36) link_BETA1-4 : bond 0.00871 ( 24) link_BETA1-4 : angle 2.26250 ( 72) hydrogen bonds : bond 0.03206 ( 1182) hydrogen bonds : angle 4.69044 ( 3216) SS BOND : bond 0.00232 ( 56) SS BOND : angle 1.44875 ( 112) covalent geometry : bond 0.00233 (34292) covalent geometry : angle 0.58659 (46704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 414 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 ASP cc_start: 0.8492 (t70) cc_final: 0.8287 (t0) REVERT: B 111 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 119 ARG cc_start: 0.8840 (mpt180) cc_final: 0.8590 (mtt90) REVERT: B 165 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: B 196 LYS cc_start: 0.7689 (ptmm) cc_final: 0.7471 (pttm) REVERT: B 232 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8491 (t-90) REVERT: B 251 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7384 (mtpp) REVERT: B 387 MET cc_start: 0.7204 (mtt) cc_final: 0.6924 (mtp) REVERT: D 114 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7944 (ptmm) REVERT: F 29 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8959 (mp) REVERT: F 31 MET cc_start: 0.9048 (mtm) cc_final: 0.8644 (mtm) REVERT: F 269 MET cc_start: 0.8747 (mtp) cc_final: 0.8494 (mtp) REVERT: F 347 LYS cc_start: 0.7596 (mtmm) cc_final: 0.7251 (mttm) REVERT: F 384 LYS cc_start: 0.6277 (ttpt) cc_final: 0.6017 (ttpt) REVERT: G 280 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: G 362 SER cc_start: 0.9070 (t) cc_final: 0.8849 (m) REVERT: G 402 MET cc_start: 0.7598 (ttp) cc_final: 0.6968 (tpt) REVERT: G 413 ILE cc_start: 0.7535 (mm) cc_final: 0.7296 (mm) REVERT: H 31 MET cc_start: 0.8995 (mtm) cc_final: 0.8745 (mtm) REVERT: H 79 LYS cc_start: 0.8477 (tttm) cc_final: 0.8234 (ttmm) REVERT: H 84 VAL cc_start: 0.9304 (t) cc_final: 0.8952 (m) REVERT: H 321 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7746 (mttp) REVERT: H 339 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9161 (mp) REVERT: H 362 SER cc_start: 0.9060 (t) cc_final: 0.8856 (m) REVERT: H 402 MET cc_start: 0.7540 (mmt) cc_final: 0.6899 (mmt) REVERT: I 53 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: I 175 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8254 (p) REVERT: I 199 TYR cc_start: 0.6264 (p90) cc_final: 0.5897 (p90) REVERT: I 223 GLU cc_start: 0.8275 (pm20) cc_final: 0.8070 (pm20) REVERT: I 224 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6387 (mt0) REVERT: J 119 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: J 178 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8021 (mmm160) REVERT: J 196 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6377 (mtpp) REVERT: K 272 GLU cc_start: 0.8905 (pm20) cc_final: 0.8636 (mp0) REVERT: K 301 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8672 (tt0) REVERT: N 8 MET cc_start: 0.6137 (pmm) cc_final: 0.5410 (pmm) REVERT: O 253 LYS cc_start: 0.8795 (tmmt) cc_final: 0.8276 (tptt) REVERT: P 227 LYS cc_start: 0.7582 (mmtm) cc_final: 0.7036 (mtpp) REVERT: Q 253 LYS cc_start: 0.7910 (tptp) cc_final: 0.7593 (tppt) outliers start: 119 outliers final: 91 residues processed: 491 average time/residue: 0.4252 time to fit residues: 346.8072 Evaluate side-chains 502 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 402 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 112 optimal weight: 0.0040 chunk 173 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 412 optimal weight: 0.1980 chunk 95 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 389 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS B 232 HIS D 201 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS L 53 GLN M 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118740 restraints weight = 40551.799| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.65 r_work: 0.3139 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 1.0389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34384 Z= 0.144 Angle : 0.650 10.710 46924 Z= 0.325 Chirality : 0.045 0.262 5296 Planarity : 0.005 0.062 5992 Dihedral : 5.638 57.618 5364 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 3.45 % Allowed : 19.25 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.76 (0.13), residues: 4244 helix: 2.91 (0.23), residues: 512 sheet: -0.36 (0.15), residues: 1172 loop : -1.35 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 235 HIS 0.006 0.001 HIS F 308 PHE 0.032 0.001 PHE K 50 TYR 0.021 0.001 TYR F 93 ARG 0.007 0.000 ARG J 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 12) link_NAG-ASN : angle 3.14306 ( 36) link_BETA1-4 : bond 0.00878 ( 24) link_BETA1-4 : angle 2.29747 ( 72) hydrogen bonds : bond 0.03439 ( 1182) hydrogen bonds : angle 4.71244 ( 3216) SS BOND : bond 0.00298 ( 56) SS BOND : angle 1.77626 ( 112) covalent geometry : bond 0.00358 (34292) covalent geometry : angle 0.63370 (46704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 402 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 ASP cc_start: 0.8495 (t70) cc_final: 0.8273 (t0) REVERT: B 119 ARG cc_start: 0.8881 (mpt180) cc_final: 0.8625 (mtt90) REVERT: B 165 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: B 196 LYS cc_start: 0.7531 (ptmm) cc_final: 0.7295 (pttm) REVERT: B 251 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7366 (mtpp) REVERT: B 387 MET cc_start: 0.7154 (mtt) cc_final: 0.6867 (mtp) REVERT: D 113 MET cc_start: 0.8125 (mmm) cc_final: 0.7563 (mmm) REVERT: D 114 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7935 (ptmm) REVERT: F 29 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8878 (mp) REVERT: F 347 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7167 (mttm) REVERT: F 384 LYS cc_start: 0.6214 (ttpt) cc_final: 0.5798 (ttpt) REVERT: G 99 GLU cc_start: 0.7904 (mp0) cc_final: 0.7670 (mm-30) REVERT: G 280 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7484 (mtp) REVERT: G 362 SER cc_start: 0.8962 (t) cc_final: 0.8744 (m) REVERT: G 402 MET cc_start: 0.7512 (ttp) cc_final: 0.6906 (tpt) REVERT: G 413 ILE cc_start: 0.7518 (mm) cc_final: 0.7296 (mm) REVERT: H 31 MET cc_start: 0.9058 (mtm) cc_final: 0.8752 (mtm) REVERT: H 42 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8912 (mt) REVERT: H 79 LYS cc_start: 0.8454 (tttm) cc_final: 0.8147 (ttmm) REVERT: H 84 VAL cc_start: 0.9259 (t) cc_final: 0.8872 (m) REVERT: H 339 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9153 (mp) REVERT: H 399 PHE cc_start: 0.9050 (t80) cc_final: 0.8842 (t80) REVERT: H 402 MET cc_start: 0.7468 (mmt) cc_final: 0.7086 (mmt) REVERT: I 175 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8163 (p) REVERT: I 199 TYR cc_start: 0.6189 (p90) cc_final: 0.5862 (p90) REVERT: I 223 GLU cc_start: 0.8275 (pm20) cc_final: 0.8060 (pm20) REVERT: I 224 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6309 (mt0) REVERT: I 251 LYS cc_start: 0.8130 (mptt) cc_final: 0.7417 (mtpp) REVERT: J 178 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7986 (mmm160) REVERT: J 196 LYS cc_start: 0.7084 (mtmt) cc_final: 0.6327 (mtpp) REVERT: J 354 ILE cc_start: 0.8025 (mm) cc_final: 0.7784 (mt) REVERT: K 272 GLU cc_start: 0.8945 (pm20) cc_final: 0.8697 (mp0) REVERT: K 301 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8588 (tt0) REVERT: K 356 GLN cc_start: 0.8635 (tt0) cc_final: 0.8158 (mt0) REVERT: N 8 MET cc_start: 0.6100 (pmm) cc_final: 0.5608 (pmm) REVERT: O 253 LYS cc_start: 0.8889 (tmmt) cc_final: 0.8251 (tptt) REVERT: P 227 LYS cc_start: 0.7650 (mmtm) cc_final: 0.7055 (mtpp) REVERT: Q 253 LYS cc_start: 0.7905 (tptp) cc_final: 0.7584 (tppt) outliers start: 125 outliers final: 102 residues processed: 486 average time/residue: 0.4142 time to fit residues: 331.9988 Evaluate side-chains 507 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 398 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 273 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 319 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 349 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 417 optimal weight: 40.0000 chunk 332 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 99 HIS J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS L 53 GLN M 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119988 restraints weight = 40560.953| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.65 r_work: 0.3155 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 1.0498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.124 Angle : 0.623 10.618 46924 Z= 0.310 Chirality : 0.044 0.257 5296 Planarity : 0.005 0.060 5992 Dihedral : 5.561 58.083 5364 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.23 % Allowed : 19.42 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.73 (0.13), residues: 4244 helix: 2.94 (0.23), residues: 512 sheet: -0.33 (0.15), residues: 1172 loop : -1.33 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 235 HIS 0.005 0.001 HIS D 186 PHE 0.031 0.001 PHE K 50 TYR 0.030 0.001 TYR I 359 ARG 0.008 0.000 ARG J 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 3.00167 ( 36) link_BETA1-4 : bond 0.00860 ( 24) link_BETA1-4 : angle 2.25804 ( 72) hydrogen bonds : bond 0.03263 ( 1182) hydrogen bonds : angle 4.65291 ( 3216) SS BOND : bond 0.00255 ( 56) SS BOND : angle 1.61647 ( 112) covalent geometry : bond 0.00302 (34292) covalent geometry : angle 0.60711 (46704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 404 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 ASP cc_start: 0.8410 (t70) cc_final: 0.8189 (t0) REVERT: B 119 ARG cc_start: 0.8913 (mpt180) cc_final: 0.8683 (mtt90) REVERT: B 165 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: B 196 LYS cc_start: 0.7561 (ptmm) cc_final: 0.7352 (pttm) REVERT: B 251 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7406 (mtpp) REVERT: B 387 MET cc_start: 0.7169 (mtt) cc_final: 0.6875 (mtp) REVERT: F 29 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8874 (mp) REVERT: F 61 LYS cc_start: 0.7484 (tttp) cc_final: 0.7257 (tttt) REVERT: F 269 MET cc_start: 0.8690 (mtp) cc_final: 0.8416 (mtp) REVERT: F 384 LYS cc_start: 0.6265 (ttpt) cc_final: 0.5933 (ttpt) REVERT: G 99 GLU cc_start: 0.7900 (mp0) cc_final: 0.7665 (mm-30) REVERT: G 160 GLN cc_start: 0.7810 (mm110) cc_final: 0.6548 (tt0) REVERT: G 280 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7324 (mtp) REVERT: G 402 MET cc_start: 0.7549 (ttp) cc_final: 0.6990 (tpt) REVERT: G 413 ILE cc_start: 0.7567 (mm) cc_final: 0.7348 (mm) REVERT: H 31 MET cc_start: 0.9063 (mtm) cc_final: 0.8782 (mtm) REVERT: H 79 LYS cc_start: 0.8469 (tttm) cc_final: 0.8157 (ttmm) REVERT: H 84 VAL cc_start: 0.9252 (t) cc_final: 0.8873 (m) REVERT: H 339 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9141 (mp) REVERT: H 402 MET cc_start: 0.7466 (mmt) cc_final: 0.7129 (mmt) REVERT: I 175 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8199 (p) REVERT: I 199 TYR cc_start: 0.6230 (p90) cc_final: 0.5904 (p90) REVERT: I 223 GLU cc_start: 0.8273 (pm20) cc_final: 0.8029 (pm20) REVERT: I 224 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6240 (mt0) REVERT: I 251 LYS cc_start: 0.8185 (mptt) cc_final: 0.7526 (mtpp) REVERT: J 13 ARG cc_start: 0.8811 (ptt90) cc_final: 0.8537 (ptt90) REVERT: J 178 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8022 (mmm160) REVERT: J 354 ILE cc_start: 0.8080 (mm) cc_final: 0.7830 (mt) REVERT: K 272 GLU cc_start: 0.8933 (pm20) cc_final: 0.8684 (mp0) REVERT: K 301 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8583 (tt0) REVERT: K 356 GLN cc_start: 0.8667 (tt0) cc_final: 0.8221 (mt0) REVERT: N 8 MET cc_start: 0.6123 (pmm) cc_final: 0.5629 (pmm) REVERT: O 253 LYS cc_start: 0.8893 (tmmt) cc_final: 0.8169 (tptt) REVERT: O 264 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8310 (m) REVERT: P 227 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7123 (mtpp) REVERT: Q 253 LYS cc_start: 0.7905 (tptp) cc_final: 0.7583 (tppt) outliers start: 117 outliers final: 99 residues processed: 481 average time/residue: 0.4395 time to fit residues: 349.5183 Evaluate side-chains 502 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 396 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 182 ASP Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 326 GLU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 264 SER Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 206 optimal weight: 10.0000 chunk 7 optimal weight: 0.0070 chunk 251 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 314 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 285 optimal weight: 0.9990 chunk 381 optimal weight: 30.0000 chunk 247 optimal weight: 0.5980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 212 ASN B 226 HIS ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS L 53 GLN M 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123293 restraints weight = 40718.175| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.22 r_work: 0.3215 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 1.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34384 Z= 0.100 Angle : 0.590 11.076 46924 Z= 0.293 Chirality : 0.043 0.247 5296 Planarity : 0.004 0.061 5992 Dihedral : 5.375 57.622 5364 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.23 % Favored : 94.65 % Rotamer: Outliers : 3.04 % Allowed : 19.61 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.60 (0.13), residues: 4244 helix: 2.97 (0.23), residues: 516 sheet: -0.20 (0.14), residues: 1256 loop : -1.29 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 170 HIS 0.005 0.001 HIS D 186 PHE 0.025 0.001 PHE K 50 TYR 0.025 0.001 TYR I 359 ARG 0.008 0.000 ARG J 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 12) link_NAG-ASN : angle 2.81423 ( 36) link_BETA1-4 : bond 0.00800 ( 24) link_BETA1-4 : angle 2.17124 ( 72) hydrogen bonds : bond 0.02927 ( 1182) hydrogen bonds : angle 4.51410 ( 3216) SS BOND : bond 0.00340 ( 56) SS BOND : angle 1.43434 ( 112) covalent geometry : bond 0.00228 (34292) covalent geometry : angle 0.57551 (46704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25976.80 seconds wall clock time: 447 minutes 45.64 seconds (26865.64 seconds total)