Starting phenix.real_space_refine on Fri Mar 6 22:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7u_73881/03_2026/9z7u_73881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7u_73881/03_2026/9z7u_73881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z7u_73881/03_2026/9z7u_73881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7u_73881/03_2026/9z7u_73881.map" model { file = "/net/cci-nas-00/data/ceres_data/9z7u_73881/03_2026/9z7u_73881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7u_73881/03_2026/9z7u_73881.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 160 5.16 5 C 20944 2.51 5 N 5624 2.21 5 O 7120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33848 Number of models: 1 Model: "" Number of chains: 32 Chain: "F" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "S" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "T" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "V" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2061 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "W" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2047 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "G" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "K" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "M" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "N" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "Q" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "S" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "T" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "V" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "W" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Time building chain proxies: 7.71, per 1000 atoms: 0.23 Number of scatterers: 33848 At special positions: 0 Unit cell: (167.433, 167.433, 118.286, 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 160 16.00 O 7120 8.00 N 5624 7.00 C 20944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.3 seconds 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8320 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 49 sheets defined 60.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 28 through 45 Processing helix chain 'F' and resid 45 through 53 removed outlier: 5.435A pdb=" N TRP F 51 " --> pdb=" O PRO F 47 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 138 through 157 Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 166 through 183 Processing helix chain 'F' and resid 200 through 208 removed outlier: 4.419A pdb=" N ARG F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 242 removed outlier: 3.712A pdb=" N ARG F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 261 removed outlier: 3.948A pdb=" N GLN F 249 " --> pdb=" O PRO F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 12 through 15 Processing helix chain 'G' and resid 28 through 45 Processing helix chain 'G' and resid 45 through 50 Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 138 through 157 Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 166 through 183 Processing helix chain 'G' and resid 200 through 208 removed outlier: 4.727A pdb=" N ARG G 205 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 243 removed outlier: 4.465A pdb=" N ARG G 232 " --> pdb=" O MET G 228 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU G 243 " --> pdb=" O MET G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 261 removed outlier: 4.516A pdb=" N GLN G 249 " --> pdb=" O PRO G 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 12 through 15 Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 45 through 53 removed outlier: 5.388A pdb=" N TRP B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 138 through 157 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.415A pdb=" N ARG B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 242 removed outlier: 3.694A pdb=" N ARG B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 removed outlier: 3.981A pdb=" N GLN B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 12 through 15 Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 138 through 157 Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 200 through 208 removed outlier: 4.699A pdb=" N ARG C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 243 removed outlier: 4.463A pdb=" N ARG C 232 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 243 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.521A pdb=" N GLN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 28 through 45 Processing helix chain 'E' and resid 45 through 53 removed outlier: 5.435A pdb=" N TRP E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 138 through 157 Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 166 through 183 Processing helix chain 'E' and resid 200 through 208 removed outlier: 4.419A pdb=" N ARG E 205 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 242 removed outlier: 3.712A pdb=" N ARG E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ALA E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 removed outlier: 3.948A pdb=" N GLN E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 12 through 15 Processing helix chain 'H' and resid 28 through 45 Processing helix chain 'H' and resid 45 through 50 Processing helix chain 'H' and resid 128 through 135 Processing helix chain 'H' and resid 138 through 157 Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 166 through 183 Processing helix chain 'H' and resid 200 through 208 removed outlier: 4.727A pdb=" N ARG H 205 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 243 removed outlier: 4.466A pdb=" N ARG H 232 " --> pdb=" O MET H 228 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H 243 " --> pdb=" O MET H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 261 removed outlier: 4.516A pdb=" N GLN H 249 " --> pdb=" O PRO H 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 11 Processing helix chain 'J' and resid 12 through 15 Processing helix chain 'J' and resid 28 through 45 Processing helix chain 'J' and resid 45 through 53 removed outlier: 5.388A pdb=" N TRP J 51 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET J 52 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 Processing helix chain 'J' and resid 138 through 157 Processing helix chain 'J' and resid 159 through 166 Processing helix chain 'J' and resid 166 through 183 Processing helix chain 'J' and resid 200 through 208 removed outlier: 4.415A pdb=" N ARG J 205 " --> pdb=" O VAL J 201 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 242 removed outlier: 3.694A pdb=" N ARG J 218 " --> pdb=" O SER J 214 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG J 232 " --> pdb=" O MET J 228 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 261 removed outlier: 3.981A pdb=" N GLN J 249 " --> pdb=" O PRO J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 278 Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 15 Processing helix chain 'K' and resid 28 through 45 Processing helix chain 'K' and resid 45 through 50 Processing helix chain 'K' and resid 128 through 135 Processing helix chain 'K' and resid 138 through 157 Processing helix chain 'K' and resid 159 through 166 Processing helix chain 'K' and resid 166 through 183 Processing helix chain 'K' and resid 200 through 208 removed outlier: 4.699A pdb=" N ARG K 205 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 243 removed outlier: 4.463A pdb=" N ARG K 232 " --> pdb=" O MET K 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU K 243 " --> pdb=" O MET K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 261 removed outlier: 4.521A pdb=" N GLN K 249 " --> pdb=" O PRO K 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 11 Processing helix chain 'M' and resid 12 through 15 Processing helix chain 'M' and resid 28 through 45 Processing helix chain 'M' and resid 45 through 53 removed outlier: 5.435A pdb=" N TRP M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET M 52 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 135 Processing helix chain 'M' and resid 138 through 157 Processing helix chain 'M' and resid 159 through 166 Processing helix chain 'M' and resid 166 through 183 Processing helix chain 'M' and resid 200 through 208 removed outlier: 4.419A pdb=" N ARG M 205 " --> pdb=" O VAL M 201 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 242 removed outlier: 3.712A pdb=" N ARG M 218 " --> pdb=" O SER M 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG M 232 " --> pdb=" O MET M 228 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA M 233 " --> pdb=" O ASN M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 245 through 261 removed outlier: 3.948A pdb=" N GLN M 249 " --> pdb=" O PRO M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 278 Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 12 through 15 Processing helix chain 'N' and resid 28 through 45 Processing helix chain 'N' and resid 45 through 50 Processing helix chain 'N' and resid 128 through 135 Processing helix chain 'N' and resid 138 through 157 Processing helix chain 'N' and resid 159 through 166 Processing helix chain 'N' and resid 166 through 183 Processing helix chain 'N' and resid 200 through 208 removed outlier: 4.727A pdb=" N ARG N 205 " --> pdb=" O VAL N 201 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 243 removed outlier: 4.466A pdb=" N ARG N 232 " --> pdb=" O MET N 228 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU N 243 " --> pdb=" O MET N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 245 through 261 removed outlier: 4.516A pdb=" N GLN N 249 " --> pdb=" O PRO N 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 11 Processing helix chain 'P' and resid 12 through 15 Processing helix chain 'P' and resid 28 through 45 Processing helix chain 'P' and resid 45 through 53 removed outlier: 5.388A pdb=" N TRP P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET P 52 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 135 Processing helix chain 'P' and resid 138 through 157 Processing helix chain 'P' and resid 159 through 166 Processing helix chain 'P' and resid 166 through 183 Processing helix chain 'P' and resid 200 through 208 removed outlier: 4.415A pdb=" N ARG P 205 " --> pdb=" O VAL P 201 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 208 through 242 removed outlier: 3.694A pdb=" N ARG P 218 " --> pdb=" O SER P 214 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG P 232 " --> pdb=" O MET P 228 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA P 233 " --> pdb=" O ASN P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 245 through 261 removed outlier: 3.981A pdb=" N GLN P 249 " --> pdb=" O PRO P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 278 Processing helix chain 'Q' and resid 6 through 11 Processing helix chain 'Q' and resid 12 through 15 Processing helix chain 'Q' and resid 28 through 45 Processing helix chain 'Q' and resid 45 through 50 Processing helix chain 'Q' and resid 128 through 135 Processing helix chain 'Q' and resid 138 through 157 Processing helix chain 'Q' and resid 159 through 166 Processing helix chain 'Q' and resid 166 through 183 Processing helix chain 'Q' and resid 200 through 208 removed outlier: 4.701A pdb=" N ARG Q 205 " --> pdb=" O VAL Q 201 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 243 removed outlier: 4.463A pdb=" N ARG Q 232 " --> pdb=" O MET Q 228 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA Q 233 " --> pdb=" O ASN Q 229 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU Q 243 " --> pdb=" O MET Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 245 through 261 removed outlier: 4.521A pdb=" N GLN Q 249 " --> pdb=" O PRO Q 245 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 11 Processing helix chain 'S' and resid 12 through 15 Processing helix chain 'S' and resid 28 through 45 Processing helix chain 'S' and resid 45 through 53 removed outlier: 5.435A pdb=" N TRP S 51 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET S 52 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 135 Processing helix chain 'S' and resid 138 through 157 Processing helix chain 'S' and resid 159 through 166 Processing helix chain 'S' and resid 166 through 183 Processing helix chain 'S' and resid 200 through 208 removed outlier: 4.419A pdb=" N ARG S 205 " --> pdb=" O VAL S 201 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA S 206 " --> pdb=" O GLN S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 242 removed outlier: 3.712A pdb=" N ARG S 218 " --> pdb=" O SER S 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG S 232 " --> pdb=" O MET S 228 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA S 233 " --> pdb=" O ASN S 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 245 through 261 removed outlier: 3.948A pdb=" N GLN S 249 " --> pdb=" O PRO S 245 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 278 Processing helix chain 'T' and resid 6 through 11 Processing helix chain 'T' and resid 12 through 15 Processing helix chain 'T' and resid 28 through 45 Processing helix chain 'T' and resid 45 through 50 Processing helix chain 'T' and resid 128 through 135 Processing helix chain 'T' and resid 138 through 157 Processing helix chain 'T' and resid 159 through 166 Processing helix chain 'T' and resid 166 through 183 Processing helix chain 'T' and resid 200 through 208 removed outlier: 4.727A pdb=" N ARG T 205 " --> pdb=" O VAL T 201 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 243 removed outlier: 4.465A pdb=" N ARG T 232 " --> pdb=" O MET T 228 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA T 233 " --> pdb=" O ASN T 229 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU T 243 " --> pdb=" O MET T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 245 through 261 removed outlier: 4.516A pdb=" N GLN T 249 " --> pdb=" O PRO T 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 11 Processing helix chain 'V' and resid 12 through 15 Processing helix chain 'V' and resid 28 through 45 Processing helix chain 'V' and resid 45 through 53 removed outlier: 5.388A pdb=" N TRP V 51 " --> pdb=" O PRO V 47 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET V 52 " --> pdb=" O ILE V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'V' and resid 138 through 157 Processing helix chain 'V' and resid 159 through 166 Processing helix chain 'V' and resid 166 through 183 Processing helix chain 'V' and resid 200 through 208 removed outlier: 4.415A pdb=" N ARG V 205 " --> pdb=" O VAL V 201 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA V 206 " --> pdb=" O GLN V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 242 removed outlier: 3.694A pdb=" N ARG V 218 " --> pdb=" O SER V 214 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG V 232 " --> pdb=" O MET V 228 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA V 233 " --> pdb=" O ASN V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 261 removed outlier: 3.981A pdb=" N GLN V 249 " --> pdb=" O PRO V 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 278 Processing helix chain 'W' and resid 6 through 11 Processing helix chain 'W' and resid 12 through 15 Processing helix chain 'W' and resid 28 through 45 Processing helix chain 'W' and resid 45 through 50 Processing helix chain 'W' and resid 128 through 135 Processing helix chain 'W' and resid 138 through 157 Processing helix chain 'W' and resid 159 through 166 Processing helix chain 'W' and resid 166 through 183 Processing helix chain 'W' and resid 200 through 208 removed outlier: 4.699A pdb=" N ARG W 205 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA W 206 " --> pdb=" O GLN W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 243 removed outlier: 4.463A pdb=" N ARG W 232 " --> pdb=" O MET W 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA W 233 " --> pdb=" O ASN W 229 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU W 243 " --> pdb=" O MET W 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 245 through 261 removed outlier: 4.521A pdb=" N GLN W 249 " --> pdb=" O PRO W 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AA3, first strand: chain 'F' and resid 99 through 109 removed outlier: 3.831A pdb=" N GLY F 120 " --> pdb=" O ILE F 103 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 118 " --> pdb=" O PRO F 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 107 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE F 116 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER F 117 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL F 197 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP F 119 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG F 125 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL F 189 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 266 through 272 removed outlier: 6.606A pdb=" N ILE F 267 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU G 271 " --> pdb=" O ILE F 267 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE F 269 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 273 " --> pdb=" O PHE F 269 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU F 271 " --> pdb=" O ILE G 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE V 267 " --> pdb=" O PHE W 269 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU W 271 " --> pdb=" O ILE V 267 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE V 269 " --> pdb=" O LEU W 271 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE W 273 " --> pdb=" O PHE V 269 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU V 271 " --> pdb=" O ILE W 273 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR S 266 " --> pdb=" O THR W 266 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL W 268 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL S 268 " --> pdb=" O VAL W 268 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE S 267 " --> pdb=" O PHE T 269 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU T 271 " --> pdb=" O ILE S 267 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE S 269 " --> pdb=" O LEU T 271 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE T 273 " --> pdb=" O PHE S 269 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU S 271 " --> pdb=" O ILE T 273 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR P 266 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL T 268 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL P 268 " --> pdb=" O VAL T 268 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE P 267 " --> pdb=" O PHE Q 269 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU Q 271 " --> pdb=" O ILE P 267 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE P 269 " --> pdb=" O LEU Q 271 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE Q 273 " --> pdb=" O PHE P 269 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU P 271 " --> pdb=" O ILE Q 273 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR M 266 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL Q 268 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL M 268 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE M 267 " --> pdb=" O PHE N 269 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU N 271 " --> pdb=" O ILE M 267 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE M 269 " --> pdb=" O LEU N 271 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE N 273 " --> pdb=" O PHE M 269 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU M 271 " --> pdb=" O ILE N 273 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR J 266 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL N 268 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL J 268 " --> pdb=" O VAL N 268 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE J 267 " --> pdb=" O PHE K 269 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU K 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE J 269 " --> pdb=" O LEU K 271 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 273 " --> pdb=" O PHE J 269 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU J 271 " --> pdb=" O ILE K 273 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR E 266 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL K 268 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 268 " --> pdb=" O VAL K 268 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE E 267 " --> pdb=" O PHE H 269 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU H 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE E 269 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 273 " --> pdb=" O PHE E 269 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU E 271 " --> pdb=" O ILE H 273 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR B 266 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL H 268 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 268 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 267 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU C 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 269 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B 271 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR F 266 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 268 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 268 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 54 through 57 Processing sheet with id=AA6, first strand: chain 'G' and resid 61 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 99 through 109 removed outlier: 3.911A pdb=" N GLY G 120 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL G 118 " --> pdb=" O PRO G 105 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU G 107 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE G 116 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER G 117 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL G 197 " --> pdb=" O SER G 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP G 119 " --> pdb=" O LYS G 195 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG G 125 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL G 189 " --> pdb=" O ARG G 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 66 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 109 removed outlier: 3.882A pdb=" N GLY B 120 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 118 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU B 107 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 116 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 117 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL B 197 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 119 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B 125 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL B 189 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 54 through 57 Processing sheet with id=AB3, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 109 removed outlier: 3.890A pdb=" N GLY C 120 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 118 " --> pdb=" O PRO C 105 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU C 107 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 116 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER C 117 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 197 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP C 119 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG C 125 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL C 189 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AB6, first strand: chain 'E' and resid 61 through 66 Processing sheet with id=AB7, first strand: chain 'E' and resid 99 through 109 removed outlier: 3.832A pdb=" N GLY E 120 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL E 118 " --> pdb=" O PRO E 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU E 107 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 116 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER E 117 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL E 197 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP E 119 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG E 125 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL E 189 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 54 through 57 Processing sheet with id=AB9, first strand: chain 'H' and resid 61 through 66 Processing sheet with id=AC1, first strand: chain 'H' and resid 99 through 109 removed outlier: 3.911A pdb=" N GLY H 120 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL H 118 " --> pdb=" O PRO H 105 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU H 107 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE H 116 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER H 117 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL H 197 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP H 119 " --> pdb=" O LYS H 195 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG H 125 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL H 189 " --> pdb=" O ARG H 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 54 through 57 Processing sheet with id=AC3, first strand: chain 'J' and resid 61 through 66 Processing sheet with id=AC4, first strand: chain 'J' and resid 99 through 109 removed outlier: 3.882A pdb=" N GLY J 120 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL J 118 " --> pdb=" O PRO J 105 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU J 107 " --> pdb=" O ILE J 116 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE J 116 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER J 117 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL J 197 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP J 119 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG J 125 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL J 189 " --> pdb=" O ARG J 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 54 through 57 Processing sheet with id=AC6, first strand: chain 'K' and resid 61 through 66 Processing sheet with id=AC7, first strand: chain 'K' and resid 99 through 109 removed outlier: 3.890A pdb=" N GLY K 120 " --> pdb=" O ILE K 103 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL K 118 " --> pdb=" O PRO K 105 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU K 107 " --> pdb=" O ILE K 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE K 116 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER K 117 " --> pdb=" O VAL K 197 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL K 197 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP K 119 " --> pdb=" O LYS K 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG K 125 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL K 189 " --> pdb=" O ARG K 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 54 through 57 Processing sheet with id=AC9, first strand: chain 'M' and resid 61 through 66 Processing sheet with id=AD1, first strand: chain 'M' and resid 99 through 109 removed outlier: 3.832A pdb=" N GLY M 120 " --> pdb=" O ILE M 103 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL M 118 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU M 107 " --> pdb=" O ILE M 116 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE M 116 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER M 117 " --> pdb=" O VAL M 197 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL M 197 " --> pdb=" O SER M 117 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP M 119 " --> pdb=" O LYS M 195 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG M 125 " --> pdb=" O VAL M 189 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL M 189 " --> pdb=" O ARG M 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 54 through 57 Processing sheet with id=AD3, first strand: chain 'N' and resid 61 through 66 Processing sheet with id=AD4, first strand: chain 'N' and resid 99 through 109 removed outlier: 3.911A pdb=" N GLY N 120 " --> pdb=" O ILE N 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL N 118 " --> pdb=" O PRO N 105 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU N 107 " --> pdb=" O ILE N 116 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE N 116 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER N 117 " --> pdb=" O VAL N 197 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL N 197 " --> pdb=" O SER N 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP N 119 " --> pdb=" O LYS N 195 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG N 125 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL N 189 " --> pdb=" O ARG N 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 54 through 57 Processing sheet with id=AD6, first strand: chain 'P' and resid 61 through 66 Processing sheet with id=AD7, first strand: chain 'P' and resid 99 through 109 removed outlier: 3.882A pdb=" N GLY P 120 " --> pdb=" O ILE P 103 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL P 118 " --> pdb=" O PRO P 105 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU P 107 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE P 116 " --> pdb=" O GLU P 107 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER P 117 " --> pdb=" O VAL P 197 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL P 197 " --> pdb=" O SER P 117 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP P 119 " --> pdb=" O LYS P 195 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG P 125 " --> pdb=" O VAL P 189 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL P 189 " --> pdb=" O ARG P 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id=AD9, first strand: chain 'Q' and resid 61 through 66 Processing sheet with id=AE1, first strand: chain 'Q' and resid 99 through 109 removed outlier: 3.890A pdb=" N GLY Q 120 " --> pdb=" O ILE Q 103 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL Q 118 " --> pdb=" O PRO Q 105 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU Q 107 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE Q 116 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER Q 117 " --> pdb=" O VAL Q 197 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL Q 197 " --> pdb=" O SER Q 117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP Q 119 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG Q 125 " --> pdb=" O VAL Q 189 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL Q 189 " --> pdb=" O ARG Q 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 54 through 57 Processing sheet with id=AE3, first strand: chain 'S' and resid 61 through 66 Processing sheet with id=AE4, first strand: chain 'S' and resid 99 through 109 removed outlier: 3.831A pdb=" N GLY S 120 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL S 118 " --> pdb=" O PRO S 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU S 107 " --> pdb=" O ILE S 116 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE S 116 " --> pdb=" O GLU S 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER S 117 " --> pdb=" O VAL S 197 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL S 197 " --> pdb=" O SER S 117 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP S 119 " --> pdb=" O LYS S 195 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG S 125 " --> pdb=" O VAL S 189 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL S 189 " --> pdb=" O ARG S 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 54 through 57 Processing sheet with id=AE6, first strand: chain 'T' and resid 61 through 66 Processing sheet with id=AE7, first strand: chain 'T' and resid 99 through 109 removed outlier: 3.911A pdb=" N GLY T 120 " --> pdb=" O ILE T 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL T 118 " --> pdb=" O PRO T 105 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU T 107 " --> pdb=" O ILE T 116 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE T 116 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER T 117 " --> pdb=" O VAL T 197 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL T 197 " --> pdb=" O SER T 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP T 119 " --> pdb=" O LYS T 195 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG T 125 " --> pdb=" O VAL T 189 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL T 189 " --> pdb=" O ARG T 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 54 through 57 Processing sheet with id=AE9, first strand: chain 'V' and resid 61 through 66 Processing sheet with id=AF1, first strand: chain 'V' and resid 99 through 109 removed outlier: 3.882A pdb=" N GLY V 120 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL V 118 " --> pdb=" O PRO V 105 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU V 107 " --> pdb=" O ILE V 116 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE V 116 " --> pdb=" O GLU V 107 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER V 117 " --> pdb=" O VAL V 197 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL V 197 " --> pdb=" O SER V 117 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP V 119 " --> pdb=" O LYS V 195 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG V 125 " --> pdb=" O VAL V 189 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL V 189 " --> pdb=" O ARG V 125 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 54 through 57 Processing sheet with id=AF3, first strand: chain 'W' and resid 61 through 66 Processing sheet with id=AF4, first strand: chain 'W' and resid 99 through 109 removed outlier: 3.890A pdb=" N GLY W 120 " --> pdb=" O ILE W 103 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL W 118 " --> pdb=" O PRO W 105 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU W 107 " --> pdb=" O ILE W 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE W 116 " --> pdb=" O GLU W 107 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER W 117 " --> pdb=" O VAL W 197 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL W 197 " --> pdb=" O SER W 117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP W 119 " --> pdb=" O LYS W 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG W 125 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL W 189 " --> pdb=" O ARG W 125 " (cutoff:3.500A) 1956 hydrogen bonds defined for protein. 5676 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: 6.70 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10848 1.34 - 1.46: 5696 1.46 - 1.58: 16512 1.58 - 1.69: 0 1.69 - 1.81: 272 Bond restraints: 33328 Sorted by residual: bond pdb=" C SER F 113 " pdb=" N VAL F 114 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.48e-02 4.57e+03 1.47e+00 bond pdb=" C SER E 113 " pdb=" N VAL E 114 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.48e-02 4.57e+03 1.33e+00 bond pdb=" C SER M 113 " pdb=" N VAL M 114 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.48e-02 4.57e+03 1.33e+00 bond pdb=" C SER J 113 " pdb=" N VAL J 114 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.48e-02 4.57e+03 1.32e+00 bond pdb=" C SER S 113 " pdb=" N VAL S 114 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.48e-02 4.57e+03 1.30e+00 ... (remaining 33323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 44791 2.47 - 4.94: 413 4.94 - 7.41: 24 7.41 - 9.88: 8 9.88 - 12.34: 4 Bond angle restraints: 45240 Sorted by residual: angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET G 52 " pdb=" CG MET G 52 " pdb=" SD MET G 52 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET T 52 " pdb=" CG MET T 52 " pdb=" SD MET T 52 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET H 52 " pdb=" CG MET H 52 " pdb=" SD MET H 52 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CA MET H 52 " pdb=" CB MET H 52 " pdb=" CG MET H 52 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 ... (remaining 45235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 18342 17.95 - 35.90: 1418 35.90 - 53.85: 420 53.85 - 71.80: 176 71.80 - 89.75: 84 Dihedral angle restraints: 20440 sinusoidal: 7728 harmonic: 12712 Sorted by residual: dihedral pdb=" CG ARG G 232 " pdb=" CD ARG G 232 " pdb=" NE ARG G 232 " pdb=" CZ ARG G 232 " ideal model delta sinusoidal sigma weight residual 90.00 41.18 48.82 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG H 232 " pdb=" CD ARG H 232 " pdb=" NE ARG H 232 " pdb=" CZ ARG H 232 " ideal model delta sinusoidal sigma weight residual 90.00 41.18 48.82 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG T 232 " pdb=" CD ARG T 232 " pdb=" NE ARG T 232 " pdb=" CZ ARG T 232 " ideal model delta sinusoidal sigma weight residual 90.00 41.18 48.82 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 20437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2832 0.027 - 0.054: 1549 0.054 - 0.080: 625 0.080 - 0.107: 352 0.107 - 0.134: 194 Chirality restraints: 5552 Sorted by residual: chirality pdb=" CA ILE J 103 " pdb=" N ILE J 103 " pdb=" C ILE J 103 " pdb=" CB ILE J 103 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE P 103 " pdb=" N ILE P 103 " pdb=" C ILE P 103 " pdb=" CB ILE P 103 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 5549 not shown) Planarity restraints: 5736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 212 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.71e+00 pdb=" C GLU F 212 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU F 212 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA F 213 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 212 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C GLU E 212 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU E 212 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA E 213 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 252 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C TYR E 252 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR E 252 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 253 " 0.009 2.00e-02 2.50e+03 ... (remaining 5733 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 21568 3.01 - 3.48: 36947 3.48 - 3.96: 60081 3.96 - 4.43: 70900 4.43 - 4.90: 106005 Nonbonded interactions: 295501 Sorted by model distance: nonbonded pdb=" N GLU N 169 " pdb=" OE1 GLU N 169 " model vdw 2.541 3.120 nonbonded pdb=" N GLU G 169 " pdb=" OE1 GLU G 169 " model vdw 2.541 3.120 nonbonded pdb=" N GLU H 169 " pdb=" OE1 GLU H 169 " model vdw 2.541 3.120 nonbonded pdb=" N GLU T 169 " pdb=" OE1 GLU T 169 " model vdw 2.541 3.120 nonbonded pdb=" N UNK B 18 " pdb=" N UNK B 19 " model vdw 2.553 2.560 ... (remaining 295496 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'B' and resid 5 through 277) selection = (chain 'C' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'E' and resid 5 through 277) selection = (chain 'F' and resid 5 through 277) selection = (chain 'G' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'H' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'J' and resid 5 through 277) selection = (chain 'K' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'M' and resid 5 through 277) selection = (chain 'N' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'P' and resid 5 through 277) selection = (chain 'Q' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'S' and resid 5 through 277) selection = (chain 'T' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) selection = (chain 'V' and resid 5 through 277) selection = (chain 'W' and (resid 5 through 275 or (resid 276 and (name N or name CA or name \ C or name O or name CB )) or resid 277)) } 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: 8.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.040 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33328 Z= 0.191 Angle : 0.648 12.344 45240 Z= 0.374 Chirality : 0.045 0.134 5552 Planarity : 0.005 0.035 5736 Dihedral : 16.792 89.747 12120 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.53 % Allowed : 18.54 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 4040 helix: 0.56 (0.11), residues: 2136 sheet: 0.46 (0.17), residues: 784 loop : -0.54 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 232 TYR 0.013 0.002 TYR S 252 PHE 0.016 0.002 PHE M 46 TRP 0.005 0.001 TRP T 185 HIS 0.001 0.000 HIS Q 172 Details of bonding type rmsd covalent geometry : bond 0.00390 (33328) covalent geometry : angle 0.64798 (45240) hydrogen bonds : bond 0.13916 ( 1956) hydrogen bonds : angle 6.69021 ( 5676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 628 time to evaluate : 1.012 Fit side-chains REVERT: F 32 TRP cc_start: 0.8035 (m100) cc_final: 0.7572 (m100) REVERT: F 46 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7685 (t80) REVERT: F 107 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 32 TRP cc_start: 0.8044 (m100) cc_final: 0.7701 (m100) REVERT: B 46 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7824 (t80) REVERT: B 67 ARG cc_start: 0.8551 (tpp-160) cc_final: 0.8290 (tpp80) REVERT: B 107 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8343 (mm-30) REVERT: B 174 MET cc_start: 0.9369 (mtm) cc_final: 0.9079 (mtm) REVERT: B 275 MET cc_start: 0.8528 (mtt) cc_final: 0.7849 (mtt) REVERT: C 56 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8616 (OUTLIER) REVERT: C 70 ARG cc_start: 0.8741 (mtp180) cc_final: 0.8356 (mtm-85) REVERT: E 32 TRP cc_start: 0.8041 (m100) cc_final: 0.7574 (m100) REVERT: E 46 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7689 (t80) REVERT: E 107 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8363 (mm-30) REVERT: J 32 TRP cc_start: 0.8042 (m100) cc_final: 0.7697 (m100) REVERT: J 46 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7820 (t80) REVERT: J 67 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8285 (tpp80) REVERT: J 107 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8353 (mm-30) REVERT: J 174 MET cc_start: 0.9365 (mtm) cc_final: 0.9075 (mtm) REVERT: J 275 MET cc_start: 0.8534 (mtt) cc_final: 0.7859 (mtt) REVERT: K 56 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8623 (OUTLIER) REVERT: K 70 ARG cc_start: 0.8742 (mtp180) cc_final: 0.8357 (mtm-85) REVERT: M 32 TRP cc_start: 0.8033 (m100) cc_final: 0.7570 (m100) REVERT: M 46 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7689 (t80) REVERT: M 107 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8362 (mm-30) REVERT: P 32 TRP cc_start: 0.8040 (m100) cc_final: 0.7695 (m100) REVERT: P 46 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7822 (t80) REVERT: P 67 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.8278 (tpp80) REVERT: P 107 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8342 (mm-30) REVERT: P 174 MET cc_start: 0.9372 (mtm) cc_final: 0.9082 (mtm) REVERT: P 275 MET cc_start: 0.8539 (mtt) cc_final: 0.7863 (mtt) REVERT: Q 56 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8618 (OUTLIER) REVERT: Q 70 ARG cc_start: 0.8747 (mtp180) cc_final: 0.8360 (mtm-85) REVERT: S 32 TRP cc_start: 0.8027 (m100) cc_final: 0.7562 (m100) REVERT: S 46 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7691 (t80) REVERT: S 107 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8363 (mm-30) REVERT: V 32 TRP cc_start: 0.8037 (m100) cc_final: 0.7693 (m100) REVERT: V 46 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7819 (t80) REVERT: V 67 ARG cc_start: 0.8546 (tpp-160) cc_final: 0.8285 (tpp80) REVERT: V 107 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8334 (mm-30) REVERT: V 174 MET cc_start: 0.9371 (mtm) cc_final: 0.9081 (mtm) REVERT: V 275 MET cc_start: 0.8540 (mtt) cc_final: 0.7865 (mtt) REVERT: W 56 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8619 (OUTLIER) REVERT: W 70 ARG cc_start: 0.8747 (mtp180) cc_final: 0.8362 (mtm-85) outliers start: 52 outliers final: 36 residues processed: 652 average time/residue: 0.6898 time to fit residues: 535.1868 Evaluate side-chains 612 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 568 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain J residue 46 PHE Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 263 LYS Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 263 LYS Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain V residue 46 PHE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 263 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN F 254 GLN F 264 ASN G 254 GLN G 277 GLN B 254 GLN C 277 GLN E 173 ASN E 254 GLN E 264 ASN H 254 GLN H 277 GLN J 254 GLN K 277 GLN M 173 ASN M 254 GLN M 264 ASN N 254 GLN N 277 GLN P 254 GLN Q 277 GLN S 173 ASN S 254 GLN S 264 ASN T 254 GLN T 277 GLN V 254 GLN W 277 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075575 restraints weight = 46279.849| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.85 r_work: 0.2801 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33328 Z= 0.241 Angle : 0.625 6.809 45240 Z= 0.338 Chirality : 0.048 0.149 5552 Planarity : 0.004 0.042 5736 Dihedral : 6.741 53.445 4708 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.40 % Allowed : 15.49 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.13), residues: 4040 helix: 1.46 (0.11), residues: 2160 sheet: 0.90 (0.18), residues: 656 loop : -0.51 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 232 TYR 0.014 0.002 TYR V 252 PHE 0.014 0.002 PHE E 46 TRP 0.006 0.001 TRP C 32 HIS 0.001 0.001 HIS T 172 Details of bonding type rmsd covalent geometry : bond 0.00556 (33328) covalent geometry : angle 0.62513 (45240) hydrogen bonds : bond 0.07390 ( 1956) hydrogen bonds : angle 4.95985 ( 5676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 526 time to evaluate : 1.309 Fit side-chains REVERT: F 32 TRP cc_start: 0.8054 (m100) cc_final: 0.7579 (m100) REVERT: F 107 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8394 (mm-30) REVERT: G 52 MET cc_start: 0.8079 (tmt) cc_final: 0.7824 (tmm) REVERT: B 32 TRP cc_start: 0.8008 (m100) cc_final: 0.7668 (m100) REVERT: B 46 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7949 (t80) REVERT: B 67 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8306 (tpp80) REVERT: B 107 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 174 MET cc_start: 0.9439 (mtm) cc_final: 0.9078 (mtm) REVERT: B 275 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7928 (mtt) REVERT: E 32 TRP cc_start: 0.8059 (m100) cc_final: 0.7583 (m100) REVERT: E 107 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8390 (mm-30) REVERT: H 52 MET cc_start: 0.8092 (tmt) cc_final: 0.7833 (tmm) REVERT: J 32 TRP cc_start: 0.8003 (m100) cc_final: 0.7665 (m100) REVERT: J 46 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7957 (t80) REVERT: J 67 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8302 (tpp80) REVERT: J 107 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8380 (mm-30) REVERT: J 174 MET cc_start: 0.9437 (mtm) cc_final: 0.9074 (mtm) REVERT: J 275 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7925 (mtt) REVERT: M 32 TRP cc_start: 0.8054 (m100) cc_final: 0.7579 (m100) REVERT: M 107 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8392 (mm-30) REVERT: N 52 MET cc_start: 0.8072 (tmt) cc_final: 0.7820 (tmm) REVERT: P 32 TRP cc_start: 0.7997 (m100) cc_final: 0.7660 (m100) REVERT: P 46 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7954 (t80) REVERT: P 67 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8302 (tpp80) REVERT: P 107 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8380 (mm-30) REVERT: P 174 MET cc_start: 0.9439 (mtm) cc_final: 0.9078 (mtm) REVERT: P 275 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7927 (mtt) REVERT: S 32 TRP cc_start: 0.8048 (m100) cc_final: 0.7573 (m100) REVERT: S 107 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8388 (mm-30) REVERT: T 52 MET cc_start: 0.8077 (tmt) cc_final: 0.7824 (tmm) REVERT: V 32 TRP cc_start: 0.7997 (m100) cc_final: 0.7658 (m100) REVERT: V 46 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7950 (t80) REVERT: V 67 ARG cc_start: 0.8618 (tpp-160) cc_final: 0.8303 (tpp80) REVERT: V 107 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8365 (mm-30) REVERT: V 174 MET cc_start: 0.9433 (mtm) cc_final: 0.9070 (mtm) REVERT: V 275 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7931 (mtt) outliers start: 116 outliers final: 64 residues processed: 602 average time/residue: 0.6947 time to fit residues: 496.5935 Evaluate side-chains 620 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 548 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain J residue 46 PHE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 136 ILE Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain V residue 46 PHE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 329 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 chunk 90 optimal weight: 0.0470 chunk 246 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 254 GLN F 264 ASN G 277 GLN B 254 GLN B 264 ASN C 254 GLN C 277 GLN E 254 GLN E 264 ASN H 277 GLN J 254 GLN J 264 ASN K 254 GLN K 277 GLN M 254 GLN M 264 ASN N 277 GLN P 254 GLN P 264 ASN Q 254 GLN Q 277 GLN S 254 GLN S 264 ASN T 277 GLN V 254 GLN V 264 ASN W 254 GLN W 277 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079096 restraints weight = 46646.379| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.88 r_work: 0.2876 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33328 Z= 0.142 Angle : 0.527 6.407 45240 Z= 0.284 Chirality : 0.044 0.150 5552 Planarity : 0.003 0.034 5736 Dihedral : 5.905 48.050 4664 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.37 % Allowed : 16.34 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4040 helix: 1.63 (0.11), residues: 2160 sheet: 1.20 (0.18), residues: 640 loop : -0.51 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 232 TYR 0.011 0.002 TYR E 252 PHE 0.013 0.001 PHE B 46 TRP 0.004 0.001 TRP B 51 HIS 0.001 0.000 HIS T 172 Details of bonding type rmsd covalent geometry : bond 0.00300 (33328) covalent geometry : angle 0.52706 (45240) hydrogen bonds : bond 0.05829 ( 1956) hydrogen bonds : angle 4.68606 ( 5676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 604 time to evaluate : 1.124 Fit side-chains REVERT: F 32 TRP cc_start: 0.8032 (m100) cc_final: 0.7529 (m100) REVERT: F 46 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7978 (t80) REVERT: F 107 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8361 (mm-30) REVERT: G 52 MET cc_start: 0.8048 (tmt) cc_final: 0.7767 (tmm) REVERT: B 32 TRP cc_start: 0.8023 (m100) cc_final: 0.7677 (m100) REVERT: B 46 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 67 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.8283 (tpp80) REVERT: B 107 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8314 (mm-30) REVERT: B 174 MET cc_start: 0.9371 (mtm) cc_final: 0.9035 (mtm) REVERT: B 275 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: C 56 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8616 (OUTLIER) REVERT: E 32 TRP cc_start: 0.8025 (m100) cc_final: 0.7524 (m100) REVERT: E 46 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7979 (t80) REVERT: E 107 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8358 (mm-30) REVERT: H 52 MET cc_start: 0.8064 (tmt) cc_final: 0.7779 (tmm) REVERT: J 32 TRP cc_start: 0.8021 (m100) cc_final: 0.7675 (m100) REVERT: J 46 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8073 (t80) REVERT: J 67 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8287 (tpp80) REVERT: J 107 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8327 (mm-30) REVERT: J 174 MET cc_start: 0.9372 (mtm) cc_final: 0.9037 (mtm) REVERT: J 275 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: K 56 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8625 (OUTLIER) REVERT: M 32 TRP cc_start: 0.8017 (m100) cc_final: 0.7516 (m100) REVERT: M 46 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7978 (t80) REVERT: M 107 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8361 (mm-30) REVERT: N 52 MET cc_start: 0.8063 (tmt) cc_final: 0.7779 (tmm) REVERT: P 32 TRP cc_start: 0.8008 (m100) cc_final: 0.7664 (m100) REVERT: P 46 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8077 (t80) REVERT: P 67 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8282 (tpp80) REVERT: P 107 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8328 (mm-30) REVERT: P 174 MET cc_start: 0.9371 (mtm) cc_final: 0.9035 (mtm) REVERT: P 275 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7751 (mtt) REVERT: Q 56 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8620 (OUTLIER) REVERT: S 32 TRP cc_start: 0.8023 (m100) cc_final: 0.7520 (m100) REVERT: S 46 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7978 (t80) REVERT: S 107 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8358 (mm-30) REVERT: T 52 MET cc_start: 0.8053 (tmt) cc_final: 0.7773 (tmm) REVERT: V 32 TRP cc_start: 0.8018 (m100) cc_final: 0.7673 (m100) REVERT: V 46 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8070 (t80) REVERT: V 67 ARG cc_start: 0.8581 (tpp-160) cc_final: 0.8288 (tpp80) REVERT: V 107 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8317 (mm-30) REVERT: V 174 MET cc_start: 0.9363 (mtm) cc_final: 0.9026 (mtm) REVERT: V 275 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: W 56 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8619 (OUTLIER) outliers start: 115 outliers final: 48 residues processed: 661 average time/residue: 0.6684 time to fit residues: 528.1180 Evaluate side-chains 606 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 546 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain J residue 46 PHE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain V residue 46 PHE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 350 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 366 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 390 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN F 254 GLN G 254 GLN G 277 GLN B 254 GLN B 264 ASN C 254 GLN C 277 GLN E 173 ASN E 254 GLN H 254 GLN H 277 GLN J 254 GLN J 264 ASN K 254 GLN K 277 GLN M 173 ASN M 254 GLN N 254 GLN N 277 GLN P 254 GLN P 264 ASN Q 254 GLN Q 277 GLN S 173 ASN S 254 GLN T 254 GLN T 277 GLN V 254 GLN V 264 ASN W 254 GLN W 277 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076907 restraints weight = 46376.193| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.88 r_work: 0.2833 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33328 Z= 0.184 Angle : 0.570 7.330 45240 Z= 0.305 Chirality : 0.045 0.148 5552 Planarity : 0.004 0.034 5736 Dihedral : 5.923 47.041 4664 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.08 % Allowed : 15.99 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4040 helix: 1.56 (0.11), residues: 2160 sheet: 1.02 (0.18), residues: 656 loop : -0.50 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 232 TYR 0.012 0.002 TYR J 252 PHE 0.011 0.001 PHE N 82 TRP 0.005 0.001 TRP B 51 HIS 0.001 0.000 HIS N 172 Details of bonding type rmsd covalent geometry : bond 0.00417 (33328) covalent geometry : angle 0.57022 (45240) hydrogen bonds : bond 0.06609 ( 1956) hydrogen bonds : angle 4.72348 ( 5676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 534 time to evaluate : 1.263 Fit side-chains REVERT: F 32 TRP cc_start: 0.8050 (m100) cc_final: 0.7554 (m100) REVERT: F 107 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8412 (mm-30) REVERT: G 52 MET cc_start: 0.8020 (tmt) cc_final: 0.7718 (tmm) REVERT: B 32 TRP cc_start: 0.8018 (m100) cc_final: 0.7668 (m100) REVERT: B 67 ARG cc_start: 0.8618 (tpp-160) cc_final: 0.8285 (tpp80) REVERT: B 107 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 174 MET cc_start: 0.9405 (mtm) cc_final: 0.9055 (mtm) REVERT: B 275 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7723 (mtt) REVERT: C 70 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8525 (mtp180) REVERT: E 32 TRP cc_start: 0.8054 (m100) cc_final: 0.7559 (m100) REVERT: E 107 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8411 (mm-30) REVERT: H 52 MET cc_start: 0.8037 (tmt) cc_final: 0.7731 (tmm) REVERT: J 32 TRP cc_start: 0.8018 (m100) cc_final: 0.7667 (m100) REVERT: J 67 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8280 (tpp80) REVERT: J 107 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8336 (mm-30) REVERT: J 174 MET cc_start: 0.9410 (mtm) cc_final: 0.9059 (mtm) REVERT: J 275 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7718 (mtt) REVERT: K 70 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8530 (mtp180) REVERT: M 32 TRP cc_start: 0.8036 (m100) cc_final: 0.7543 (m100) REVERT: M 107 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8413 (mm-30) REVERT: N 52 MET cc_start: 0.8023 (tmt) cc_final: 0.7720 (tmm) REVERT: P 32 TRP cc_start: 0.8015 (m100) cc_final: 0.7666 (m100) REVERT: P 67 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8281 (tpp80) REVERT: P 107 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8339 (mm-30) REVERT: P 174 MET cc_start: 0.9406 (mtm) cc_final: 0.9056 (mtm) REVERT: P 275 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7758 (mtt) REVERT: Q 70 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8526 (mtp180) REVERT: S 32 TRP cc_start: 0.8038 (m100) cc_final: 0.7542 (m100) REVERT: S 107 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8412 (mm-30) REVERT: T 52 MET cc_start: 0.8024 (tmt) cc_final: 0.7720 (tmm) REVERT: V 32 TRP cc_start: 0.8011 (m100) cc_final: 0.7661 (m100) REVERT: V 67 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8278 (tpp80) REVERT: V 107 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8333 (mm-30) REVERT: V 174 MET cc_start: 0.9403 (mtm) cc_final: 0.9053 (mtm) REVERT: V 275 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7753 (mtt) REVERT: W 70 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8529 (mtp180) outliers start: 139 outliers final: 66 residues processed: 613 average time/residue: 0.6963 time to fit residues: 507.0621 Evaluate side-chains 617 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 543 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 127 GLN Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 70 ARG Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 127 GLN Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 67 optimal weight: 0.4980 chunk 322 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 368 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 356 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN F 254 GLN F 264 ASN G 254 GLN G 277 GLN B 254 GLN B 264 ASN C 254 GLN C 277 GLN E 173 ASN E 254 GLN E 264 ASN H 254 GLN H 277 GLN J 254 GLN J 264 ASN K 254 GLN K 277 GLN M 173 ASN M 254 GLN M 264 ASN N 254 GLN N 277 GLN P 254 GLN P 264 ASN Q 254 GLN Q 277 GLN S 173 ASN S 254 GLN S 264 ASN T 254 GLN T 277 GLN V 254 GLN V 264 ASN W 254 GLN W 277 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.114188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079481 restraints weight = 46658.797| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.90 r_work: 0.2890 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33328 Z= 0.137 Angle : 0.522 6.716 45240 Z= 0.280 Chirality : 0.044 0.148 5552 Planarity : 0.003 0.034 5736 Dihedral : 5.442 47.411 4648 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.35 % Allowed : 18.02 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.13), residues: 4040 helix: 1.63 (0.11), residues: 2160 sheet: 1.24 (0.18), residues: 640 loop : -0.57 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 232 TYR 0.011 0.001 TYR M 252 PHE 0.011 0.001 PHE V 46 TRP 0.006 0.001 TRP V 51 HIS 0.001 0.000 HIS G 172 Details of bonding type rmsd covalent geometry : bond 0.00293 (33328) covalent geometry : angle 0.52226 (45240) hydrogen bonds : bond 0.05627 ( 1956) hydrogen bonds : angle 4.59789 ( 5676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 574 time to evaluate : 1.330 Fit side-chains REVERT: F 32 TRP cc_start: 0.8043 (m100) cc_final: 0.7539 (m100) REVERT: F 107 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8423 (mm-30) REVERT: G 52 MET cc_start: 0.7983 (tmt) cc_final: 0.7676 (tmm) REVERT: G 56 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 32 TRP cc_start: 0.8031 (m100) cc_final: 0.7678 (m100) REVERT: B 107 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8365 (mm-30) REVERT: B 174 MET cc_start: 0.9350 (mtm) cc_final: 0.9033 (mtm) REVERT: B 275 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7700 (mtt) REVERT: C 56 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8624 (OUTLIER) REVERT: C 67 ARG cc_start: 0.8551 (tpp-160) cc_final: 0.8338 (tpp-160) REVERT: E 32 TRP cc_start: 0.8043 (m100) cc_final: 0.7542 (m100) REVERT: E 107 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8425 (mm-30) REVERT: H 52 MET cc_start: 0.8007 (tmt) cc_final: 0.7693 (tmm) REVERT: H 56 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8708 (mt) REVERT: J 32 TRP cc_start: 0.8032 (m100) cc_final: 0.7677 (m100) REVERT: J 107 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8362 (mm-30) REVERT: J 174 MET cc_start: 0.9357 (mtm) cc_final: 0.9043 (mtm) REVERT: J 275 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7689 (mtt) REVERT: K 56 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8634 (OUTLIER) REVERT: K 67 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8334 (tpp-160) REVERT: M 32 TRP cc_start: 0.8028 (m100) cc_final: 0.7525 (m100) REVERT: M 107 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8424 (mm-30) REVERT: N 52 MET cc_start: 0.7998 (tmt) cc_final: 0.7687 (tmm) REVERT: N 56 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8708 (mt) REVERT: P 32 TRP cc_start: 0.8035 (m100) cc_final: 0.7682 (m100) REVERT: P 107 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8365 (mm-30) REVERT: P 174 MET cc_start: 0.9357 (mtm) cc_final: 0.9042 (mtm) REVERT: Q 56 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8629 (OUTLIER) REVERT: Q 67 ARG cc_start: 0.8546 (tpp-160) cc_final: 0.8332 (tpp-160) REVERT: S 32 TRP cc_start: 0.8029 (m100) cc_final: 0.7525 (m100) REVERT: S 107 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8419 (mm-30) REVERT: T 52 MET cc_start: 0.8000 (tmt) cc_final: 0.7685 (tmm) REVERT: T 56 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8711 (mt) REVERT: V 32 TRP cc_start: 0.8034 (m100) cc_final: 0.7681 (m100) REVERT: V 107 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8352 (mm-30) REVERT: V 174 MET cc_start: 0.9344 (mtm) cc_final: 0.9026 (mtm) REVERT: W 56 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8628 (OUTLIER) REVERT: W 67 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8335 (tpp-160) outliers start: 114 outliers final: 60 residues processed: 626 average time/residue: 0.6379 time to fit residues: 479.6328 Evaluate side-chains 650 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 584 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain V residue 259 ILE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 392 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 269 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 323 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 ASN G 277 GLN B 254 GLN B 264 ASN C 254 GLN C 277 GLN H 277 GLN J 254 GLN J 264 ASN K 254 GLN K 277 GLN N 277 GLN P 254 GLN P 264 ASN Q 254 GLN Q 277 GLN T 277 GLN V 254 GLN V 264 ASN W 254 GLN W 277 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078127 restraints weight = 46326.602| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.86 r_work: 0.2857 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33328 Z= 0.162 Angle : 0.551 7.237 45240 Z= 0.296 Chirality : 0.045 0.146 5552 Planarity : 0.004 0.033 5736 Dihedral : 5.472 48.005 4648 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.05 % Allowed : 18.43 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4040 helix: 1.63 (0.11), residues: 2160 sheet: 1.26 (0.18), residues: 640 loop : -0.56 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 232 TYR 0.011 0.002 TYR M 252 PHE 0.011 0.001 PHE T 82 TRP 0.006 0.001 TRP B 51 HIS 0.001 0.000 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00362 (33328) covalent geometry : angle 0.55089 (45240) hydrogen bonds : bond 0.06167 ( 1956) hydrogen bonds : angle 4.65855 ( 5676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 571 time to evaluate : 1.204 Fit side-chains REVERT: F 32 TRP cc_start: 0.8063 (m100) cc_final: 0.7560 (m100) REVERT: F 107 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8433 (mm-30) REVERT: G 52 MET cc_start: 0.8111 (tmt) cc_final: 0.7775 (tmm) REVERT: G 67 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8442 (tpp-160) REVERT: B 32 TRP cc_start: 0.8060 (m100) cc_final: 0.7703 (m100) REVERT: B 107 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 174 MET cc_start: 0.9379 (mtm) cc_final: 0.9045 (mtm) REVERT: B 275 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: C 56 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8634 (OUTLIER) REVERT: E 32 TRP cc_start: 0.8065 (m100) cc_final: 0.7563 (m100) REVERT: E 107 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8444 (mm-30) REVERT: H 52 MET cc_start: 0.8133 (tmt) cc_final: 0.7792 (tmm) REVERT: H 67 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8439 (tpp-160) REVERT: J 32 TRP cc_start: 0.8066 (m100) cc_final: 0.7708 (m100) REVERT: J 107 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8380 (mm-30) REVERT: J 174 MET cc_start: 0.9385 (mtm) cc_final: 0.9053 (mtm) REVERT: J 275 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7716 (mtt) REVERT: K 56 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8639 (OUTLIER) REVERT: M 32 TRP cc_start: 0.8046 (m100) cc_final: 0.7543 (m100) REVERT: M 107 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8445 (mm-30) REVERT: N 52 MET cc_start: 0.8135 (tmt) cc_final: 0.7793 (tmm) REVERT: N 67 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8439 (tpp-160) REVERT: P 32 TRP cc_start: 0.8068 (m100) cc_final: 0.7711 (m100) REVERT: P 107 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8383 (mm-30) REVERT: P 174 MET cc_start: 0.9380 (mtm) cc_final: 0.9049 (mtm) REVERT: Q 56 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8639 (OUTLIER) REVERT: S 32 TRP cc_start: 0.8050 (m100) cc_final: 0.7545 (m100) REVERT: S 107 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8433 (mm-30) REVERT: T 52 MET cc_start: 0.8128 (tmt) cc_final: 0.7788 (tmm) REVERT: T 67 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8445 (tpp-160) REVERT: V 32 TRP cc_start: 0.8058 (m100) cc_final: 0.7701 (m100) REVERT: V 107 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8372 (mm-30) REVERT: V 174 MET cc_start: 0.9371 (mtm) cc_final: 0.9038 (mtm) REVERT: W 56 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8640 (OUTLIER) outliers start: 104 outliers final: 66 residues processed: 623 average time/residue: 0.6508 time to fit residues: 485.5722 Evaluate side-chains 630 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 562 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain V residue 259 ILE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 387 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 322 optimal weight: 0.7980 chunk 362 optimal weight: 1.9990 chunk 398 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 ASN G 254 GLN G 277 GLN B 254 GLN B 264 ASN C 277 GLN E 264 ASN H 254 GLN H 277 GLN J 254 GLN J 264 ASN K 277 GLN M 264 ASN N 254 GLN N 277 GLN P 254 GLN P 264 ASN Q 277 GLN S 264 ASN T 254 GLN T 277 GLN V 254 GLN V 264 ASN W 277 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.079543 restraints weight = 46627.739| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.90 r_work: 0.2891 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33328 Z= 0.139 Angle : 0.534 7.863 45240 Z= 0.285 Chirality : 0.044 0.146 5552 Planarity : 0.003 0.033 5736 Dihedral : 5.370 47.108 4648 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.32 % Allowed : 18.46 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.13), residues: 4040 helix: 1.67 (0.11), residues: 2160 sheet: 1.29 (0.18), residues: 640 loop : -0.62 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 232 TYR 0.011 0.001 TYR S 252 PHE 0.016 0.001 PHE M 39 TRP 0.005 0.001 TRP N 32 HIS 0.000 0.000 HIS T 172 Details of bonding type rmsd covalent geometry : bond 0.00302 (33328) covalent geometry : angle 0.53423 (45240) hydrogen bonds : bond 0.05631 ( 1956) hydrogen bonds : angle 4.60673 ( 5676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 564 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 32 TRP cc_start: 0.8054 (m100) cc_final: 0.7518 (m100) REVERT: F 107 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8417 (mm-30) REVERT: G 52 MET cc_start: 0.8096 (tmt) cc_final: 0.7754 (tmm) REVERT: B 32 TRP cc_start: 0.8063 (m100) cc_final: 0.7711 (m100) REVERT: B 107 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 174 MET cc_start: 0.9335 (mtm) cc_final: 0.9019 (mtm) REVERT: B 275 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: C 56 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8651 (mt) REVERT: E 32 TRP cc_start: 0.8058 (m100) cc_final: 0.7523 (m100) REVERT: E 107 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8423 (mm-30) REVERT: H 52 MET cc_start: 0.8116 (tmt) cc_final: 0.7769 (tmm) REVERT: J 32 TRP cc_start: 0.8063 (m100) cc_final: 0.7708 (m100) REVERT: J 107 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8369 (mm-30) REVERT: J 174 MET cc_start: 0.9342 (mtm) cc_final: 0.9026 (mtm) REVERT: J 275 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7656 (mtt) REVERT: K 56 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8657 (mt) REVERT: M 32 TRP cc_start: 0.8040 (m100) cc_final: 0.7502 (m100) REVERT: M 107 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8428 (mm-30) REVERT: N 52 MET cc_start: 0.8117 (tmt) cc_final: 0.7770 (tmm) REVERT: P 32 TRP cc_start: 0.8062 (m100) cc_final: 0.7709 (m100) REVERT: P 107 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8370 (mm-30) REVERT: P 174 MET cc_start: 0.9341 (mtm) cc_final: 0.9026 (mtm) REVERT: Q 56 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8654 (mt) REVERT: S 32 TRP cc_start: 0.8037 (m100) cc_final: 0.7498 (m100) REVERT: S 107 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8420 (mm-30) REVERT: T 52 MET cc_start: 0.8108 (tmt) cc_final: 0.7765 (tmm) REVERT: V 32 TRP cc_start: 0.8051 (m100) cc_final: 0.7698 (m100) REVERT: V 107 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8364 (mm-30) REVERT: V 174 MET cc_start: 0.9332 (mtm) cc_final: 0.9017 (mtm) REVERT: W 56 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8657 (mt) outliers start: 113 outliers final: 70 residues processed: 624 average time/residue: 0.6733 time to fit residues: 502.1206 Evaluate side-chains 636 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 560 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 259 ILE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 415 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 chunk 245 optimal weight: 0.0970 chunk 402 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN B 254 GLN B 264 ASN C 254 GLN C 277 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN J 254 GLN J 264 ASN K 254 GLN K 277 GLN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 277 GLN P 254 GLN P 264 ASN Q 254 GLN Q 277 GLN ** S 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN V 254 GLN V 264 ASN W 254 GLN W 277 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.078547 restraints weight = 46393.562| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.88 r_work: 0.2868 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33328 Z= 0.155 Angle : 0.547 7.949 45240 Z= 0.294 Chirality : 0.044 0.144 5552 Planarity : 0.004 0.033 5736 Dihedral : 5.393 47.149 4648 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.08 % Allowed : 18.90 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 4040 helix: 1.64 (0.11), residues: 2160 sheet: 1.28 (0.18), residues: 640 loop : -0.57 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 232 TYR 0.011 0.002 TYR M 252 PHE 0.012 0.001 PHE F 39 TRP 0.005 0.001 TRP G 32 HIS 0.001 0.000 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00348 (33328) covalent geometry : angle 0.54696 (45240) hydrogen bonds : bond 0.06008 ( 1956) hydrogen bonds : angle 4.65862 ( 5676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 555 time to evaluate : 1.195 Fit side-chains REVERT: F 32 TRP cc_start: 0.8094 (m100) cc_final: 0.7538 (m100) REVERT: F 107 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8421 (mm-30) REVERT: G 52 MET cc_start: 0.8129 (tmt) cc_final: 0.7809 (tmm) REVERT: B 32 TRP cc_start: 0.8084 (m100) cc_final: 0.7733 (m100) REVERT: B 107 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 174 MET cc_start: 0.9367 (mtm) cc_final: 0.9040 (mtm) REVERT: B 275 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7686 (mtt) REVERT: C 56 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8635 (OUTLIER) REVERT: E 32 TRP cc_start: 0.8091 (m100) cc_final: 0.7535 (m100) REVERT: E 107 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8435 (mm-30) REVERT: H 52 MET cc_start: 0.8136 (tmt) cc_final: 0.7814 (tmm) REVERT: J 32 TRP cc_start: 0.8082 (m100) cc_final: 0.7729 (m100) REVERT: J 107 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8383 (mm-30) REVERT: J 174 MET cc_start: 0.9380 (mtm) cc_final: 0.9054 (mtm) REVERT: J 275 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: K 56 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8633 (OUTLIER) REVERT: M 32 TRP cc_start: 0.8067 (m100) cc_final: 0.7511 (m100) REVERT: M 107 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8442 (mm-30) REVERT: N 52 MET cc_start: 0.8138 (tmt) cc_final: 0.7817 (tmm) REVERT: P 32 TRP cc_start: 0.8082 (m100) cc_final: 0.7729 (m100) REVERT: P 107 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8381 (mm-30) REVERT: P 174 MET cc_start: 0.9373 (mtm) cc_final: 0.9050 (mtm) REVERT: P 275 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7657 (mtt) REVERT: Q 56 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8630 (OUTLIER) REVERT: S 32 TRP cc_start: 0.8073 (m100) cc_final: 0.7515 (m100) REVERT: S 107 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8426 (mm-30) REVERT: T 52 MET cc_start: 0.8132 (tmt) cc_final: 0.7812 (tmm) REVERT: V 32 TRP cc_start: 0.8078 (m100) cc_final: 0.7725 (m100) REVERT: V 107 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8374 (mm-30) REVERT: V 174 MET cc_start: 0.9364 (mtm) cc_final: 0.9041 (mtm) REVERT: V 275 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7652 (mtt) REVERT: W 56 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8638 (OUTLIER) outliers start: 105 outliers final: 76 residues processed: 604 average time/residue: 0.6585 time to fit residues: 477.1146 Evaluate side-chains 600 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 520 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 259 ILE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 54 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 171 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 339 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 336 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN B 264 ASN C 277 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN J 264 ASN K 277 GLN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 254 GLN N 277 GLN P 264 ASN Q 277 GLN ** S 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN V 264 ASN W 277 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077507 restraints weight = 46146.622| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.89 r_work: 0.2848 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33328 Z= 0.177 Angle : 0.579 8.650 45240 Z= 0.309 Chirality : 0.045 0.140 5552 Planarity : 0.004 0.034 5736 Dihedral : 5.458 46.440 4648 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.70 % Allowed : 19.37 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.13), residues: 4040 helix: 1.61 (0.11), residues: 2160 sheet: 1.26 (0.18), residues: 640 loop : -0.55 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 232 TYR 0.011 0.002 TYR M 252 PHE 0.010 0.001 PHE B 46 TRP 0.005 0.001 TRP C 32 HIS 0.001 0.000 HIS T 172 Details of bonding type rmsd covalent geometry : bond 0.00405 (33328) covalent geometry : angle 0.57888 (45240) hydrogen bonds : bond 0.06365 ( 1956) hydrogen bonds : angle 4.71332 ( 5676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 509 time to evaluate : 1.210 Fit side-chains REVERT: F 32 TRP cc_start: 0.8092 (m100) cc_final: 0.7546 (m100) REVERT: F 107 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8447 (mm-30) REVERT: G 52 MET cc_start: 0.8164 (tmt) cc_final: 0.7815 (tmm) REVERT: B 32 TRP cc_start: 0.8074 (m100) cc_final: 0.7720 (m100) REVERT: B 107 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 174 MET cc_start: 0.9398 (mtm) cc_final: 0.9053 (mtm) REVERT: B 275 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: C 56 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8620 (mt) REVERT: E 32 TRP cc_start: 0.8102 (m100) cc_final: 0.7554 (m100) REVERT: E 107 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8448 (mm-30) REVERT: H 52 MET cc_start: 0.8174 (tmt) cc_final: 0.7822 (tmm) REVERT: J 32 TRP cc_start: 0.8070 (m100) cc_final: 0.7715 (m100) REVERT: J 107 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8398 (mm-30) REVERT: J 174 MET cc_start: 0.9405 (mtm) cc_final: 0.9061 (mtm) REVERT: J 275 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: K 56 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8625 (mt) REVERT: M 32 TRP cc_start: 0.8079 (m100) cc_final: 0.7534 (m100) REVERT: M 107 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8442 (mm-30) REVERT: N 52 MET cc_start: 0.8165 (tmt) cc_final: 0.7816 (tmm) REVERT: P 32 TRP cc_start: 0.8074 (m100) cc_final: 0.7720 (m100) REVERT: P 107 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8401 (mm-30) REVERT: P 174 MET cc_start: 0.9400 (mtm) cc_final: 0.9058 (mtm) REVERT: P 275 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7673 (mtt) REVERT: Q 56 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8622 (mt) REVERT: S 32 TRP cc_start: 0.8083 (m100) cc_final: 0.7537 (m100) REVERT: S 107 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8442 (mm-30) REVERT: T 52 MET cc_start: 0.8153 (tmt) cc_final: 0.7807 (tmm) REVERT: V 32 TRP cc_start: 0.8062 (m100) cc_final: 0.7709 (m100) REVERT: V 107 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8391 (mm-30) REVERT: V 174 MET cc_start: 0.9392 (mtm) cc_final: 0.9048 (mtm) REVERT: V 275 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7682 (mtt) REVERT: W 56 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8623 (mt) outliers start: 92 outliers final: 68 residues processed: 559 average time/residue: 0.6947 time to fit residues: 461.8659 Evaluate side-chains 613 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 537 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 259 ILE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 54 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 106 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 289 optimal weight: 0.0670 chunk 306 optimal weight: 0.9980 chunk 243 optimal weight: 20.0000 chunk 317 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 277 GLN B 264 ASN C 254 GLN C 277 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 254 GLN H 277 GLN J 264 ASN K 254 GLN K 277 GLN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 277 GLN P 264 ASN Q 254 GLN Q 277 GLN ** S 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 254 GLN T 277 GLN V 264 ASN W 254 GLN W 277 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.078413 restraints weight = 46439.746| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.88 r_work: 0.2865 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33328 Z= 0.160 Angle : 0.549 8.687 45240 Z= 0.295 Chirality : 0.045 0.142 5552 Planarity : 0.004 0.035 5736 Dihedral : 5.389 46.194 4648 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.61 % Allowed : 19.40 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 4040 helix: 1.64 (0.11), residues: 2160 sheet: 1.27 (0.18), residues: 640 loop : -0.55 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 232 TYR 0.011 0.002 TYR S 252 PHE 0.010 0.001 PHE E 39 TRP 0.005 0.001 TRP C 32 HIS 0.000 0.000 HIS E 172 Details of bonding type rmsd covalent geometry : bond 0.00359 (33328) covalent geometry : angle 0.54872 (45240) hydrogen bonds : bond 0.06039 ( 1956) hydrogen bonds : angle 4.66649 ( 5676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 540 time to evaluate : 1.300 Fit side-chains REVERT: F 32 TRP cc_start: 0.8093 (m100) cc_final: 0.7551 (m100) REVERT: F 107 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8427 (mm-30) REVERT: G 52 MET cc_start: 0.8167 (tmt) cc_final: 0.7819 (tmm) REVERT: B 32 TRP cc_start: 0.8094 (m100) cc_final: 0.7738 (m100) REVERT: B 107 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B 174 MET cc_start: 0.9385 (mtm) cc_final: 0.9052 (mtm) REVERT: B 275 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7631 (mtt) REVERT: C 52 MET cc_start: 0.7924 (tmt) cc_final: 0.7667 (tmm) REVERT: C 56 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8635 (OUTLIER) REVERT: E 32 TRP cc_start: 0.8102 (m100) cc_final: 0.7559 (m100) REVERT: E 107 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8448 (mm-30) REVERT: H 52 MET cc_start: 0.8166 (tmt) cc_final: 0.7816 (tmm) REVERT: J 32 TRP cc_start: 0.8089 (m100) cc_final: 0.7732 (m100) REVERT: J 107 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8379 (mm-30) REVERT: J 174 MET cc_start: 0.9393 (mtm) cc_final: 0.9062 (mtm) REVERT: J 275 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: K 52 MET cc_start: 0.7904 (tmt) cc_final: 0.7653 (tmm) REVERT: K 56 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8637 (OUTLIER) REVERT: M 32 TRP cc_start: 0.8085 (m100) cc_final: 0.7544 (m100) REVERT: M 107 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8433 (mm-30) REVERT: N 52 MET cc_start: 0.8161 (tmt) cc_final: 0.7813 (tmm) REVERT: P 32 TRP cc_start: 0.8091 (m100) cc_final: 0.7735 (m100) REVERT: P 107 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8384 (mm-30) REVERT: P 174 MET cc_start: 0.9389 (mtm) cc_final: 0.9060 (mtm) REVERT: P 275 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: Q 52 MET cc_start: 0.7922 (tmt) cc_final: 0.7666 (tmm) REVERT: Q 56 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8662 (mt) REVERT: S 32 TRP cc_start: 0.8083 (m100) cc_final: 0.7541 (m100) REVERT: S 107 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8429 (mm-30) REVERT: T 52 MET cc_start: 0.8162 (tmt) cc_final: 0.7814 (tmm) REVERT: V 32 TRP cc_start: 0.8086 (m100) cc_final: 0.7729 (m100) REVERT: V 107 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8372 (mm-30) REVERT: V 174 MET cc_start: 0.9375 (mtm) cc_final: 0.9044 (mtm) REVERT: V 275 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7671 (mtt) REVERT: W 52 MET cc_start: 0.7918 (tmt) cc_final: 0.7664 (tmm) REVERT: W 56 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8661 (mt) outliers start: 89 outliers final: 68 residues processed: 588 average time/residue: 0.6718 time to fit residues: 471.8849 Evaluate side-chains 575 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 501 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 32 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 275 MET Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain N residue 32 TRP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 102 ASP Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 275 MET Chi-restraints excluded: chain Q residue 32 TRP Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain T residue 32 TRP Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 102 ASP Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 259 ILE Chi-restraints excluded: chain V residue 275 MET Chi-restraints excluded: chain W residue 32 TRP Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 412 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 374 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 402 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 378 optimal weight: 20.0000 chunk 416 optimal weight: 1.9990 chunk 297 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN B 264 ASN C 277 GLN E 173 ASN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN J 264 ASN K 277 GLN M 173 ASN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 254 GLN N 277 GLN P 264 ASN Q 277 GLN S 173 ASN ** S 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN V 264 ASN W 277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075481 restraints weight = 46101.585| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.92 r_work: 0.2797 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33328 Z= 0.254 Angle : 0.638 8.249 45240 Z= 0.341 Chirality : 0.048 0.143 5552 Planarity : 0.004 0.041 5736 Dihedral : 5.620 45.318 4648 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.44 % Allowed : 19.63 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4040 helix: 1.57 (0.11), residues: 2160 sheet: 1.15 (0.18), residues: 648 loop : -0.48 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 232 TYR 0.012 0.002 TYR B 252 PHE 0.013 0.002 PHE V 269 TRP 0.005 0.001 TRP C 32 HIS 0.001 0.000 HIS G 172 Details of bonding type rmsd covalent geometry : bond 0.00601 (33328) covalent geometry : angle 0.63751 (45240) hydrogen bonds : bond 0.07346 ( 1956) hydrogen bonds : angle 4.84995 ( 5676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19011.88 seconds wall clock time: 321 minutes 47.03 seconds (19307.03 seconds total)