Starting phenix.real_space_refine on Fri Mar 6 05:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cy8_27070/03_2026/8cy8_27070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cy8_27070/03_2026/8cy8_27070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cy8_27070/03_2026/8cy8_27070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cy8_27070/03_2026/8cy8_27070.map" model { file = "/net/cci-nas-00/data/ceres_data/8cy8_27070/03_2026/8cy8_27070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cy8_27070/03_2026/8cy8_27070.cif" } resolution = 2.94 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= 0.095 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 192 5.16 5 C 18264 2.51 5 N 4884 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 28800 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "E" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "G" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "H" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "I" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "J" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "K" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "L" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.24 Number of scatterers: 28800 At special positions: 0 Unit cell: (153.34, 150.88, 138.58, 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 192 16.00 O 5460 8.00 N 4884 7.00 C 18264 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 12 sheets defined 67.9% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.704A pdb=" N LYS A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 13 through 18' Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.614A pdb=" N ALA A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 161 through 173 Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.759A pdb=" N PHE A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 243 removed outlier: 4.114A pdb=" N ILE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 253 through 268 Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 269 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.687A pdb=" N ASP A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.691A pdb=" N ALA A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.525A pdb=" N LYS B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.785A pdb=" N ALA B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 96 through 99 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 161 through 173 Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 201 through 218 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.190A pdb=" N ILE B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 253 through 268 Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 269 through 285 Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.729A pdb=" N ASP B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.708A pdb=" N LYS C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 18 " --> pdb=" O ASN C 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 18' Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.724A pdb=" N ALA C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 86 through 95 removed outlier: 3.502A pdb=" N ASN C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 99 Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 184 through 199 Processing helix chain 'C' and resid 201 through 218 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 232 through 243 removed outlier: 4.094A pdb=" N ILE C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 253 through 268 Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.775A pdb=" N ASP C 312 " --> pdb=" O LYS C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.664A pdb=" N ALA C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.842A pdb=" N LYS D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.760A pdb=" N ALA D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 96 through 99 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 184 through 199 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.200A pdb=" N ILE D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 253 through 268 Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 269 through 285 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.763A pdb=" N ASP D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.708A pdb=" N ALA D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 Processing helix chain 'E' and resid 12 through 18 removed outlier: 4.408A pdb=" N ILE E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER E 18 " --> pdb=" O ASN E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 removed outlier: 3.746A pdb=" N ALA E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 86 through 95 Processing helix chain 'E' and resid 96 through 99 Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 134 through 141 Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.510A pdb=" N ILE E 173 " --> pdb=" O TYR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 199 Processing helix chain 'E' and resid 201 through 218 Processing helix chain 'E' and resid 221 through 230 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.156A pdb=" N ILE E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 253 through 268 Proline residue: E 265 - end of helix Processing helix chain 'E' and resid 269 through 285 Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.700A pdb=" N ASP E 312 " --> pdb=" O LYS E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.685A pdb=" N ALA E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 12 removed outlier: 6.934A pdb=" N ASP F 12 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 18 removed outlier: 3.623A pdb=" N LYS F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 13 through 18' Processing helix chain 'F' and resid 27 through 39 removed outlier: 3.850A pdb=" N ALA F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 83 through 95 removed outlier: 4.747A pdb=" N ALA F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 99 Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 134 through 141 Processing helix chain 'F' and resid 161 through 173 Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 201 through 218 Processing helix chain 'F' and resid 221 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.109A pdb=" N ILE F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 253 through 268 Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 269 through 285 Processing helix chain 'F' and resid 286 through 298 Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.710A pdb=" N ASP F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 removed outlier: 3.710A pdb=" N ALA F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.848A pdb=" N LYS G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER G 18 " --> pdb=" O ASN G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 27 through 39 removed outlier: 3.810A pdb=" N ALA G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 86 through 95 Processing helix chain 'G' and resid 96 through 99 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 134 through 141 Processing helix chain 'G' and resid 161 through 173 Processing helix chain 'G' and resid 184 through 199 Processing helix chain 'G' and resid 201 through 218 Processing helix chain 'G' and resid 221 through 230 Processing helix chain 'G' and resid 232 through 243 removed outlier: 4.093A pdb=" N ILE G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 253 through 268 Proline residue: G 265 - end of helix Processing helix chain 'G' and resid 269 through 285 Processing helix chain 'G' and resid 286 through 298 Processing helix chain 'G' and resid 300 through 312 removed outlier: 3.769A pdb=" N ASP G 312 " --> pdb=" O LYS G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 324 removed outlier: 3.686A pdb=" N ALA G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 11 Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.769A pdb=" N LYS H 17 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 18 " --> pdb=" O ASN H 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 18' Processing helix chain 'H' and resid 27 through 39 removed outlier: 3.750A pdb=" N ALA H 32 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 75 Processing helix chain 'H' and resid 83 through 95 removed outlier: 4.721A pdb=" N ALA H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 99 Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'H' and resid 134 through 141 Processing helix chain 'H' and resid 161 through 173 Processing helix chain 'H' and resid 184 through 199 Processing helix chain 'H' and resid 201 through 218 Processing helix chain 'H' and resid 221 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.170A pdb=" N ILE H 236 " --> pdb=" O GLU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 253 through 268 Proline residue: H 265 - end of helix Processing helix chain 'H' and resid 269 through 285 Processing helix chain 'H' and resid 286 through 298 Processing helix chain 'H' and resid 300 through 312 removed outlier: 3.675A pdb=" N ASP H 312 " --> pdb=" O LYS H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 323 Processing helix chain 'I' and resid 7 through 12 removed outlier: 6.902A pdb=" N ASP I 12 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 18 removed outlier: 3.509A pdb=" N LYS I 17 " --> pdb=" O LEU I 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER I 18 " --> pdb=" O ASN I 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 13 through 18' Processing helix chain 'I' and resid 27 through 38 removed outlier: 3.671A pdb=" N ALA I 32 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 67 through 75 Processing helix chain 'I' and resid 86 through 95 Processing helix chain 'I' and resid 96 through 99 Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 134 through 141 Processing helix chain 'I' and resid 161 through 173 Processing helix chain 'I' and resid 184 through 199 Processing helix chain 'I' and resid 201 through 218 Processing helix chain 'I' and resid 221 through 230 Processing helix chain 'I' and resid 232 through 243 removed outlier: 4.132A pdb=" N ILE I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 252 Processing helix chain 'I' and resid 253 through 268 Proline residue: I 265 - end of helix Processing helix chain 'I' and resid 269 through 285 Processing helix chain 'I' and resid 286 through 298 Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.696A pdb=" N ASP I 312 " --> pdb=" O LYS I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 324 removed outlier: 3.682A pdb=" N ALA I 324 " --> pdb=" O ARG I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 27 through 38 removed outlier: 3.772A pdb=" N ALA J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 41 No H-bonds generated for 'chain 'J' and resid 39 through 41' Processing helix chain 'J' and resid 67 through 75 Processing helix chain 'J' and resid 86 through 95 Processing helix chain 'J' and resid 96 through 99 Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 134 through 141 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 184 through 199 Processing helix chain 'J' and resid 201 through 218 Processing helix chain 'J' and resid 221 through 230 Processing helix chain 'J' and resid 232 through 243 removed outlier: 4.132A pdb=" N ILE J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 252 Processing helix chain 'J' and resid 253 through 268 Proline residue: J 265 - end of helix Processing helix chain 'J' and resid 269 through 285 Processing helix chain 'J' and resid 286 through 298 Processing helix chain 'J' and resid 300 through 312 removed outlier: 3.695A pdb=" N ASP J 312 " --> pdb=" O LYS J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 324 removed outlier: 3.696A pdb=" N ALA J 324 " --> pdb=" O ARG J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 13 through 18 removed outlier: 3.773A pdb=" N LYS K 17 " --> pdb=" O LEU K 13 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER K 18 " --> pdb=" O ASN K 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 13 through 18' Processing helix chain 'K' and resid 27 through 38 removed outlier: 3.770A pdb=" N ALA K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 67 through 75 Processing helix chain 'K' and resid 83 through 95 removed outlier: 4.765A pdb=" N ALA K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 99 Processing helix chain 'K' and resid 110 through 115 Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 161 through 173 removed outlier: 3.505A pdb=" N ILE K 173 " --> pdb=" O TYR K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 199 removed outlier: 3.544A pdb=" N GLU K 196 " --> pdb=" O ASP K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 218 Processing helix chain 'K' and resid 221 through 230 Processing helix chain 'K' and resid 232 through 243 removed outlier: 4.082A pdb=" N ILE K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 253 through 268 Proline residue: K 265 - end of helix Processing helix chain 'K' and resid 269 through 285 Processing helix chain 'K' and resid 286 through 298 Processing helix chain 'K' and resid 300 through 312 removed outlier: 3.793A pdb=" N ASP K 312 " --> pdb=" O LYS K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 324 removed outlier: 3.684A pdb=" N ALA K 324 " --> pdb=" O ARG K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 13 through 18 removed outlier: 3.853A pdb=" N LYS L 17 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER L 18 " --> pdb=" O ASN L 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 13 through 18' Processing helix chain 'L' and resid 27 through 38 removed outlier: 3.701A pdb=" N ALA L 32 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 41 No H-bonds generated for 'chain 'L' and resid 39 through 41' Processing helix chain 'L' and resid 67 through 75 Processing helix chain 'L' and resid 83 through 95 removed outlier: 4.723A pdb=" N ALA L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 99 Processing helix chain 'L' and resid 110 through 115 Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 161 through 173 Processing helix chain 'L' and resid 184 through 199 Processing helix chain 'L' and resid 201 through 218 Processing helix chain 'L' and resid 221 through 230 Processing helix chain 'L' and resid 232 through 243 removed outlier: 4.115A pdb=" N ILE L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 252 Processing helix chain 'L' and resid 253 through 268 Proline residue: L 265 - end of helix Processing helix chain 'L' and resid 269 through 285 Processing helix chain 'L' and resid 286 through 298 Processing helix chain 'L' and resid 300 through 312 removed outlier: 3.802A pdb=" N ASP L 312 " --> pdb=" O LYS L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 324 removed outlier: 3.678A pdb=" N ALA L 324 " --> pdb=" O ARG L 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.742A pdb=" N CYS A 150 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 78 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS A 20 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET A 79 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 22 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N MET A 66 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 46 " --> pdb=" O MET A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.730A pdb=" N CYS B 150 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 78 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N MET B 66 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 46 " --> pdb=" O MET B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.700A pdb=" N CYS C 150 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 78 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS C 20 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET C 79 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA C 22 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N MET C 66 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 46 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.742A pdb=" N CYS D 150 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 78 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS D 20 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N MET D 79 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA D 22 " --> pdb=" O MET D 79 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N MET D 66 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 46 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 6 removed outlier: 6.322A pdb=" N ILE E 78 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N MET E 66 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE E 46 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 removed outlier: 6.703A pdb=" N CYS F 150 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE F 78 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS F 20 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET F 79 " --> pdb=" O LYS F 20 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA F 22 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N MET F 66 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE F 46 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 6 removed outlier: 6.752A pdb=" N CYS G 150 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE G 78 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS G 20 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET G 79 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA G 22 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N MET G 66 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE G 46 " --> pdb=" O MET G 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 5 through 6 removed outlier: 6.728A pdb=" N CYS H 150 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE H 78 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS H 20 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET H 79 " --> pdb=" O LYS H 20 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA H 22 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N MET H 66 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE H 46 " --> pdb=" O MET H 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 5 through 6 removed outlier: 6.710A pdb=" N CYS I 150 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE I 78 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS I 20 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N MET I 79 " --> pdb=" O LYS I 20 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA I 22 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N MET I 66 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE I 46 " --> pdb=" O MET I 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 5 through 6 removed outlier: 6.704A pdb=" N CYS J 150 " --> pdb=" O ILE J 181 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE J 78 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N MET J 66 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE J 46 " --> pdb=" O MET J 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 6 removed outlier: 6.706A pdb=" N CYS K 150 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE K 78 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS K 20 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET K 79 " --> pdb=" O LYS K 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA K 22 " --> pdb=" O MET K 79 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N MET K 66 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE K 46 " --> pdb=" O MET K 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 6 removed outlier: 6.755A pdb=" N CYS L 150 " --> pdb=" O ILE L 181 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE L 78 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N MET L 66 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE L 46 " --> pdb=" O MET L 66 " (cutoff:3.500A) 1701 hydrogen bonds defined for protein. 4947 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: 6.10 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4992 1.30 - 1.43: 6974 1.43 - 1.55: 16942 1.55 - 1.68: 0 1.68 - 1.81: 336 Bond restraints: 29244 Sorted by residual: bond pdb=" CG GLN E 197 " pdb=" CD GLN E 197 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.74e+00 bond pdb=" CB ASP D 125 " pdb=" CG ASP D 125 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG GLN C 197 " pdb=" CD GLN C 197 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.62e+00 bond pdb=" CB ASP I 125 " pdb=" CG ASP I 125 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" CB ASP L 125 " pdb=" CG ASP L 125 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 ... (remaining 29239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 37846 1.75 - 3.50: 1310 3.50 - 5.24: 133 5.24 - 6.99: 52 6.99 - 8.74: 19 Bond angle restraints: 39360 Sorted by residual: angle pdb=" CG MET A 35 " pdb=" SD MET A 35 " pdb=" CE MET A 35 " ideal model delta sigma weight residual 100.90 94.46 6.44 2.20e+00 2.07e-01 8.56e+00 angle pdb=" CB MET C 35 " pdb=" CG MET C 35 " pdb=" SD MET C 35 " ideal model delta sigma weight residual 112.70 120.89 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" CB MET I 79 " pdb=" CG MET I 79 " pdb=" SD MET I 79 " ideal model delta sigma weight residual 112.70 120.51 -7.81 3.00e+00 1.11e-01 6.78e+00 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 120.42 -7.72 3.00e+00 1.11e-01 6.62e+00 angle pdb=" CG MET F 35 " pdb=" SD MET F 35 " pdb=" CE MET F 35 " ideal model delta sigma weight residual 100.90 95.26 5.64 2.20e+00 2.07e-01 6.57e+00 ... (remaining 39355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16341 17.99 - 35.98: 1068 35.98 - 53.97: 176 53.97 - 71.96: 46 71.96 - 89.95: 21 Dihedral angle restraints: 17652 sinusoidal: 7008 harmonic: 10644 Sorted by residual: dihedral pdb=" CB GLU E 295 " pdb=" CG GLU E 295 " pdb=" CD GLU E 295 " pdb=" OE1 GLU E 295 " ideal model delta sinusoidal sigma weight residual 0.00 89.95 -89.95 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 295 " pdb=" CG GLU A 295 " pdb=" CD GLU A 295 " pdb=" OE1 GLU A 295 " ideal model delta sinusoidal sigma weight residual 0.00 88.96 -88.96 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU D 295 " pdb=" CG GLU D 295 " pdb=" CD GLU D 295 " pdb=" OE1 GLU D 295 " ideal model delta sinusoidal sigma weight residual 0.00 -87.38 87.38 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1798 0.033 - 0.065: 1509 0.065 - 0.098: 748 0.098 - 0.130: 343 0.130 - 0.163: 54 Chirality restraints: 4452 Sorted by residual: chirality pdb=" CA GLU D 94 " pdb=" N GLU D 94 " pdb=" C GLU D 94 " pdb=" CB GLU D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA GLU J 94 " pdb=" N GLU J 94 " pdb=" C GLU J 94 " pdb=" CB GLU J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4449 not shown) Planarity restraints: 5076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 31 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C HIS F 31 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS F 31 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA F 32 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA J 130 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO J 131 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 131 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 131 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 264 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 265 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.023 5.00e-02 4.00e+02 ... (remaining 5073 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1175 2.72 - 3.26: 28044 3.26 - 3.81: 43574 3.81 - 4.35: 55462 4.35 - 4.90: 97441 Nonbonded interactions: 225696 Sorted by model distance: nonbonded pdb=" O ALA C 32 " pdb=" ND2 ASN C 36 " model vdw 2.171 3.120 nonbonded pdb=" N GLY D 123 " pdb=" OE1 GLU D 158 " model vdw 2.204 3.120 nonbonded pdb=" OE1 GLU C 190 " pdb=" OH TYR D 220 " model vdw 2.209 3.040 nonbonded pdb=" N GLY J 123 " pdb=" OE1 GLU J 158 " model vdw 2.217 3.120 nonbonded pdb=" N GLY F 123 " pdb=" OE1 GLU F 158 " model vdw 2.219 3.120 ... (remaining 225691 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 330) selection = (chain 'B' and resid 3 through 330) selection = chain 'C' selection = (chain 'D' and resid 3 through 330) selection = (chain 'E' and resid 3 through 330) selection = (chain 'F' and resid 3 through 330) selection = (chain 'G' and resid 3 through 330) selection = (chain 'H' and resid 3 through 330) selection = (chain 'I' and resid 3 through 330) selection = (chain 'J' and resid 3 through 330) selection = (chain 'K' and resid 3 through 330) selection = (chain 'L' and resid 3 through 330) } 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: 7.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.050 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.011 0.061 29244 Z= 0.427 Angle : 0.785 8.737 39360 Z= 0.423 Chirality : 0.056 0.163 4452 Planarity : 0.006 0.045 5076 Dihedral : 12.769 89.946 10836 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.60 (0.14), residues: 3672 helix: 1.32 (0.11), residues: 2208 sheet: 1.60 (0.24), residues: 492 loop : 0.39 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 38 TYR 0.021 0.003 TYR J 241 PHE 0.020 0.003 PHE I 288 TRP 0.022 0.004 TRP E 328 HIS 0.011 0.002 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.01050 (29244) covalent geometry : angle 0.78539 (39360) hydrogen bonds : bond 0.24326 ( 1701) hydrogen bonds : angle 6.06150 ( 4947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 31 HIS cc_start: 0.6524 (t-90) cc_final: 0.5917 (t-90) REVERT: A 35 MET cc_start: 0.7362 (mpp) cc_final: 0.6894 (mpt) REVERT: A 66 MET cc_start: 0.7447 (pmm) cc_final: 0.7148 (pmm) REVERT: A 128 MET cc_start: 0.8992 (ttp) cc_final: 0.8770 (ttp) REVERT: B 66 MET cc_start: 0.7511 (pmm) cc_final: 0.7296 (pmm) REVERT: B 224 MET cc_start: 0.8412 (mmp) cc_final: 0.8092 (mmp) REVERT: C 36 ASN cc_start: 0.8214 (m-40) cc_final: 0.7785 (m110) REVERT: C 188 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7881 (tp30) REVERT: C 224 MET cc_start: 0.8303 (mmp) cc_final: 0.8091 (mmp) REVERT: D 36 ASN cc_start: 0.8036 (m110) cc_final: 0.7769 (m-40) REVERT: E 36 ASN cc_start: 0.7946 (m110) cc_final: 0.7437 (m110) REVERT: F 36 ASN cc_start: 0.8203 (m110) cc_final: 0.7860 (m110) REVERT: H 36 ASN cc_start: 0.7749 (m110) cc_final: 0.7331 (m110) REVERT: H 66 MET cc_start: 0.7462 (pmm) cc_final: 0.7123 (pmm) REVERT: J 224 MET cc_start: 0.8357 (mmp) cc_final: 0.8068 (mmp) REVERT: J 247 ASP cc_start: 0.7571 (t70) cc_final: 0.7369 (t0) REVERT: K 66 MET cc_start: 0.7504 (pmm) cc_final: 0.7222 (pmm) REVERT: L 36 ASN cc_start: 0.7994 (m110) cc_final: 0.7606 (m110) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.7252 time to fit residues: 430.1924 Evaluate side-chains 442 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 242 GLN F 242 GLN G 242 GLN H 242 GLN I 242 GLN I 311 ASN J 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122507 restraints weight = 33403.829| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.03 r_work: 0.3236 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29244 Z= 0.111 Angle : 0.474 7.707 39360 Z= 0.256 Chirality : 0.043 0.138 4452 Planarity : 0.004 0.035 5076 Dihedral : 4.560 78.805 4008 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.79 % Allowed : 7.80 % Favored : 91.40 % 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: 1.87 (0.14), residues: 3672 helix: 1.57 (0.11), residues: 2256 sheet: 1.68 (0.24), residues: 492 loop : 0.34 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 297 TYR 0.008 0.001 TYR D 115 PHE 0.010 0.001 PHE E 288 TRP 0.012 0.002 TRP E 328 HIS 0.006 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00250 (29244) covalent geometry : angle 0.47437 (39360) hydrogen bonds : bond 0.04278 ( 1701) hydrogen bonds : angle 4.32316 ( 4947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 469 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.9055 (ttp) cc_final: 0.8820 (ttp) REVERT: B 35 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6472 (mpt) REVERT: B 66 MET cc_start: 0.7452 (pmm) cc_final: 0.6943 (pmm) REVERT: B 101 GLU cc_start: 0.7015 (mp0) cc_final: 0.6746 (mp0) REVERT: B 274 LYS cc_start: 0.8352 (mptt) cc_final: 0.8034 (mtmt) REVERT: C 36 ASN cc_start: 0.7469 (m-40) cc_final: 0.7060 (m110) REVERT: C 316 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8085 (mm-30) REVERT: D 35 MET cc_start: 0.6804 (mpt) cc_final: 0.6585 (mpt) REVERT: D 36 ASN cc_start: 0.7337 (m110) cc_final: 0.6854 (m110) REVERT: D 66 MET cc_start: 0.7043 (pmm) cc_final: 0.6316 (pmm) REVERT: D 79 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7306 (tpp) REVERT: E 36 ASN cc_start: 0.7695 (m110) cc_final: 0.7188 (m-40) REVERT: E 192 ASP cc_start: 0.8287 (t70) cc_final: 0.7939 (t0) REVERT: F 48 LEU cc_start: 0.8688 (mt) cc_final: 0.8481 (mp) REVERT: G 66 MET cc_start: 0.7440 (pmm) cc_final: 0.6964 (pmm) REVERT: G 192 ASP cc_start: 0.8245 (t70) cc_final: 0.7776 (t0) REVERT: H 36 ASN cc_start: 0.7387 (m110) cc_final: 0.6761 (m110) REVERT: H 48 LEU cc_start: 0.8631 (mt) cc_final: 0.8386 (mp) REVERT: H 66 MET cc_start: 0.7390 (pmm) cc_final: 0.6885 (pmm) REVERT: I 66 MET cc_start: 0.7216 (pmm) cc_final: 0.6474 (pmm) REVERT: K 66 MET cc_start: 0.7517 (pmm) cc_final: 0.7076 (pmm) REVERT: L 36 ASN cc_start: 0.7510 (m110) cc_final: 0.7062 (m110) REVERT: L 266 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8491 (mttt) outliers start: 24 outliers final: 1 residues processed: 472 average time/residue: 0.7152 time to fit residues: 390.0849 Evaluate side-chains 443 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 439 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain L residue 266 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 338 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 14 optimal weight: 0.2980 chunk 281 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 197 GLN A 242 GLN F 242 GLN G 242 GLN H 31 HIS I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.162314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120658 restraints weight = 33672.698| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.84 r_work: 0.3201 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29244 Z= 0.169 Angle : 0.522 9.328 39360 Z= 0.281 Chirality : 0.045 0.140 4452 Planarity : 0.004 0.036 5076 Dihedral : 4.475 65.925 4008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.36 % Allowed : 9.52 % Favored : 89.12 % 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: 1.73 (0.14), residues: 3672 helix: 1.57 (0.11), residues: 2220 sheet: 1.60 (0.24), residues: 492 loop : 0.03 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.010 0.001 TYR D 115 PHE 0.014 0.002 PHE I 288 TRP 0.011 0.002 TRP E 328 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00418 (29244) covalent geometry : angle 0.52212 (39360) hydrogen bonds : bond 0.05355 ( 1701) hydrogen bonds : angle 4.33204 ( 4947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 463 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: A 128 MET cc_start: 0.9087 (ttp) cc_final: 0.8872 (ttp) REVERT: B 66 MET cc_start: 0.7477 (pmm) cc_final: 0.6914 (pmm) REVERT: B 271 GLU cc_start: 0.7732 (mp0) cc_final: 0.7464 (mt-10) REVERT: B 274 LYS cc_start: 0.8440 (mptt) cc_final: 0.8084 (mtmt) REVERT: C 36 ASN cc_start: 0.7835 (m-40) cc_final: 0.7399 (m110) REVERT: D 36 ASN cc_start: 0.7483 (m110) cc_final: 0.7027 (m110) REVERT: D 66 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6358 (pmm) REVERT: D 79 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7480 (tpp) REVERT: D 180 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7409 (mp) REVERT: E 36 ASN cc_start: 0.7734 (m110) cc_final: 0.7206 (m-40) REVERT: E 128 MET cc_start: 0.9147 (ttm) cc_final: 0.8874 (ttp) REVERT: E 192 ASP cc_start: 0.8388 (t70) cc_final: 0.8026 (t0) REVERT: E 271 GLU cc_start: 0.7682 (mp0) cc_final: 0.7378 (mt-10) REVERT: F 36 ASN cc_start: 0.7812 (m110) cc_final: 0.7368 (m110) REVERT: G 35 MET cc_start: 0.7098 (mmm) cc_final: 0.6347 (mpm) REVERT: G 66 MET cc_start: 0.7422 (pmm) cc_final: 0.6909 (pmm) REVERT: G 192 ASP cc_start: 0.8330 (t70) cc_final: 0.7905 (t0) REVERT: G 242 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7708 (mp-120) REVERT: H 36 ASN cc_start: 0.7493 (m110) cc_final: 0.7028 (m110) REVERT: H 66 MET cc_start: 0.7415 (pmm) cc_final: 0.6833 (pmm) REVERT: H 271 GLU cc_start: 0.7848 (mp0) cc_final: 0.7543 (mt-10) REVERT: I 66 MET cc_start: 0.7351 (pmm) cc_final: 0.7123 (pmt) REVERT: I 247 ASP cc_start: 0.7924 (t70) cc_final: 0.7388 (OUTLIER) REVERT: I 266 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8579 (mttt) REVERT: J 48 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8340 (mt) REVERT: J 224 MET cc_start: 0.8669 (mmp) cc_final: 0.8463 (mmp) REVERT: K 31 HIS cc_start: 0.6755 (t-90) cc_final: 0.6426 (m170) REVERT: K 84 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7260 (t70) REVERT: K 271 GLU cc_start: 0.7849 (mp0) cc_final: 0.7543 (mt-10) REVERT: L 36 ASN cc_start: 0.7667 (m110) cc_final: 0.7246 (m110) REVERT: L 271 GLU cc_start: 0.7830 (mp0) cc_final: 0.7467 (mm-30) REVERT: L 325 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.4937 (mpt) outliers start: 41 outliers final: 7 residues processed: 475 average time/residue: 0.7603 time to fit residues: 416.7410 Evaluate side-chains 468 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 453 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 242 GLN Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 178 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 368 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN B 242 GLN D 161 ASN F 242 GLN G 242 GLN H 31 HIS I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119893 restraints weight = 33595.021| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.06 r_work: 0.3182 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 29244 Z= 0.176 Angle : 0.530 8.482 39360 Z= 0.285 Chirality : 0.045 0.134 4452 Planarity : 0.004 0.038 5076 Dihedral : 4.445 54.260 4008 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.39 % Allowed : 10.32 % Favored : 88.29 % 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: 1.63 (0.14), residues: 3672 helix: 1.52 (0.11), residues: 2220 sheet: 1.48 (0.24), residues: 492 loop : -0.06 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 38 TYR 0.010 0.001 TYR D 115 PHE 0.014 0.002 PHE E 288 TRP 0.010 0.002 TRP F 328 HIS 0.005 0.001 HIS J 31 Details of bonding type rmsd covalent geometry : bond 0.00437 (29244) covalent geometry : angle 0.52995 (39360) hydrogen bonds : bond 0.05338 ( 1701) hydrogen bonds : angle 4.32662 ( 4947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 467 time to evaluate : 1.133 Fit side-chains REVERT: A 128 MET cc_start: 0.9114 (ttp) cc_final: 0.8893 (ttp) REVERT: B 35 MET cc_start: 0.6811 (mpt) cc_final: 0.5768 (mpt) REVERT: B 66 MET cc_start: 0.7404 (pmm) cc_final: 0.6828 (pmm) REVERT: B 271 GLU cc_start: 0.7792 (mp0) cc_final: 0.7534 (mt-10) REVERT: B 274 LYS cc_start: 0.8498 (mptt) cc_final: 0.8156 (mtmt) REVERT: C 36 ASN cc_start: 0.7915 (m-40) cc_final: 0.7437 (m110) REVERT: C 101 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6737 (mm-30) REVERT: C 247 ASP cc_start: 0.7878 (t70) cc_final: 0.7337 (t0) REVERT: C 271 GLU cc_start: 0.7891 (mp0) cc_final: 0.7631 (mt-10) REVERT: D 36 ASN cc_start: 0.7544 (m110) cc_final: 0.7102 (m110) REVERT: D 79 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7491 (tpp) REVERT: D 101 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6517 (mm-30) REVERT: E 36 ASN cc_start: 0.7814 (m110) cc_final: 0.7304 (m-40) REVERT: E 79 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7481 (tpp) REVERT: E 101 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6311 (mm-30) REVERT: E 128 MET cc_start: 0.9170 (ttm) cc_final: 0.8932 (ttp) REVERT: E 192 ASP cc_start: 0.8437 (t70) cc_final: 0.8098 (t0) REVERT: E 271 GLU cc_start: 0.7761 (mp0) cc_final: 0.7457 (mt-10) REVERT: F 36 ASN cc_start: 0.7894 (m110) cc_final: 0.7465 (m110) REVERT: F 247 ASP cc_start: 0.7866 (t70) cc_final: 0.7498 (t70) REVERT: G 35 MET cc_start: 0.7280 (mmm) cc_final: 0.6896 (mpm) REVERT: G 66 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6899 (pmm) REVERT: G 192 ASP cc_start: 0.8371 (t70) cc_final: 0.7963 (t0) REVERT: G 250 TYR cc_start: 0.8034 (t80) cc_final: 0.7569 (m-10) REVERT: H 31 HIS cc_start: 0.6867 (t-170) cc_final: 0.6566 (t70) REVERT: H 36 ASN cc_start: 0.7742 (m110) cc_final: 0.7285 (m110) REVERT: H 66 MET cc_start: 0.7396 (pmm) cc_final: 0.6837 (pmm) REVERT: H 271 GLU cc_start: 0.7934 (mp0) cc_final: 0.7658 (mt-10) REVERT: I 266 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8632 (mttt) REVERT: J 38 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.5882 (ttm-80) REVERT: J 48 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8379 (mt) REVERT: J 266 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8691 (mttt) REVERT: K 66 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6608 (pmm) REVERT: K 76 ASP cc_start: 0.7787 (t70) cc_final: 0.7173 (t0) REVERT: K 84 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7279 (t70) REVERT: K 247 ASP cc_start: 0.7964 (t70) cc_final: 0.7435 (t0) REVERT: K 271 GLU cc_start: 0.7927 (mp0) cc_final: 0.7648 (mt-10) REVERT: L 36 ASN cc_start: 0.7686 (m110) cc_final: 0.7282 (m110) REVERT: L 101 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6329 (mm-30) REVERT: L 192 ASP cc_start: 0.8366 (t70) cc_final: 0.7977 (t0) REVERT: L 271 GLU cc_start: 0.7891 (mp0) cc_final: 0.7545 (mm-30) REVERT: L 325 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5095 (mpt) outliers start: 42 outliers final: 8 residues processed: 478 average time/residue: 0.7393 time to fit residues: 409.1817 Evaluate side-chains 469 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 447 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain E residue 79 MET Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 78 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 255 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 242 GLN D 161 ASN F 242 GLN G 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118331 restraints weight = 33574.183| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.94 r_work: 0.3224 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29244 Z= 0.136 Angle : 0.495 8.719 39360 Z= 0.265 Chirality : 0.043 0.132 4452 Planarity : 0.003 0.038 5076 Dihedral : 4.274 50.265 4008 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.39 % Allowed : 11.08 % Favored : 87.53 % 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: 1.81 (0.14), residues: 3672 helix: 1.69 (0.11), residues: 2220 sheet: 1.46 (0.24), residues: 492 loop : 0.00 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 249 TYR 0.009 0.001 TYR D 115 PHE 0.012 0.001 PHE E 288 TRP 0.009 0.002 TRP F 328 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00328 (29244) covalent geometry : angle 0.49542 (39360) hydrogen bonds : bond 0.04561 ( 1701) hydrogen bonds : angle 4.23997 ( 4947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 463 time to evaluate : 1.174 Fit side-chains REVERT: A 66 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6750 (pmm) REVERT: A 101 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 128 MET cc_start: 0.9076 (ttp) cc_final: 0.8749 (ttp) REVERT: B 35 MET cc_start: 0.6794 (mpt) cc_final: 0.6580 (mpt) REVERT: B 66 MET cc_start: 0.7523 (pmm) cc_final: 0.6981 (pmm) REVERT: B 274 LYS cc_start: 0.8432 (mptt) cc_final: 0.8096 (mtmt) REVERT: C 36 ASN cc_start: 0.7742 (m-40) cc_final: 0.7268 (m110) REVERT: C 247 ASP cc_start: 0.7847 (t70) cc_final: 0.7291 (t0) REVERT: C 250 TYR cc_start: 0.8075 (t80) cc_final: 0.7471 (m-10) REVERT: D 36 ASN cc_start: 0.7406 (m110) cc_final: 0.6947 (m110) REVERT: D 66 MET cc_start: 0.7149 (pmm) cc_final: 0.6923 (pmt) REVERT: D 79 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7433 (tpp) REVERT: D 101 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6404 (mm-30) REVERT: E 36 ASN cc_start: 0.7767 (m110) cc_final: 0.7238 (m-40) REVERT: E 76 ASP cc_start: 0.7608 (t70) cc_final: 0.6943 (t0) REVERT: E 101 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6267 (mm-30) REVERT: E 128 MET cc_start: 0.9159 (ttm) cc_final: 0.8899 (ttp) REVERT: E 192 ASP cc_start: 0.8339 (t70) cc_final: 0.7976 (t0) REVERT: F 36 ASN cc_start: 0.7888 (m110) cc_final: 0.7444 (m110) REVERT: F 247 ASP cc_start: 0.7758 (t70) cc_final: 0.7378 (t70) REVERT: F 271 GLU cc_start: 0.7769 (mp0) cc_final: 0.7410 (mt-10) REVERT: G 35 MET cc_start: 0.7241 (mmm) cc_final: 0.6890 (mpm) REVERT: G 66 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6899 (pmm) REVERT: G 192 ASP cc_start: 0.8284 (t70) cc_final: 0.7873 (t0) REVERT: G 250 TYR cc_start: 0.7976 (t80) cc_final: 0.7448 (m-10) REVERT: H 36 ASN cc_start: 0.7550 (m110) cc_final: 0.7033 (m110) REVERT: H 66 MET cc_start: 0.7414 (pmm) cc_final: 0.6801 (pmm) REVERT: I 247 ASP cc_start: 0.7897 (t70) cc_final: 0.7375 (t0) REVERT: I 266 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8555 (mttt) REVERT: J 38 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5439 (ttm-80) REVERT: J 48 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8359 (mt) REVERT: J 266 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8564 (mttt) REVERT: L 6 TYR cc_start: 0.7925 (m-80) cc_final: 0.7656 (m-80) REVERT: L 36 ASN cc_start: 0.7565 (m110) cc_final: 0.7145 (m110) REVERT: L 85 GLU cc_start: 0.7601 (mp0) cc_final: 0.7296 (mp0) REVERT: L 101 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6271 (mm-30) REVERT: L 250 TYR cc_start: 0.8109 (t80) cc_final: 0.7501 (m-10) REVERT: L 325 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.5026 (mpt) outliers start: 42 outliers final: 8 residues processed: 479 average time/residue: 0.7091 time to fit residues: 395.3877 Evaluate side-chains 463 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 443 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 242 GLN Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 349 optimal weight: 0.6980 chunk 352 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 242 GLN D 161 ASN G 242 GLN I 242 GLN J 242 GLN K 161 ASN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118339 restraints weight = 33539.099| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.13 r_work: 0.3124 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 29244 Z= 0.223 Angle : 0.590 9.301 39360 Z= 0.313 Chirality : 0.046 0.134 4452 Planarity : 0.004 0.040 5076 Dihedral : 4.563 48.819 4008 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.79 % Allowed : 12.70 % Favored : 85.52 % 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: 1.41 (0.14), residues: 3672 helix: 1.35 (0.11), residues: 2232 sheet: 1.24 (0.24), residues: 492 loop : -0.08 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 297 TYR 0.013 0.002 TYR G 241 PHE 0.016 0.002 PHE E 288 TRP 0.011 0.002 TRP E 328 HIS 0.005 0.001 HIS J 31 Details of bonding type rmsd covalent geometry : bond 0.00561 (29244) covalent geometry : angle 0.58988 (39360) hydrogen bonds : bond 0.06038 ( 1701) hydrogen bonds : angle 4.39981 ( 4947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 469 time to evaluate : 1.062 Fit side-chains REVERT: A 31 HIS cc_start: 0.6850 (t70) cc_final: 0.5977 (m170) REVERT: A 35 MET cc_start: 0.6621 (mmt) cc_final: 0.6268 (mmt) REVERT: A 101 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: A 128 MET cc_start: 0.9146 (ttp) cc_final: 0.8885 (ttp) REVERT: B 66 MET cc_start: 0.7468 (pmm) cc_final: 0.6971 (pmm) REVERT: B 224 MET cc_start: 0.8888 (mmp) cc_final: 0.8574 (mmp) REVERT: B 247 ASP cc_start: 0.7784 (t0) cc_final: 0.7510 (t0) REVERT: B 271 GLU cc_start: 0.7830 (mp0) cc_final: 0.7584 (mt-10) REVERT: C 36 ASN cc_start: 0.7908 (m-40) cc_final: 0.7448 (m110) REVERT: C 101 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6425 (mm-30) REVERT: C 128 MET cc_start: 0.9134 (ttp) cc_final: 0.8923 (ttm) REVERT: C 247 ASP cc_start: 0.7997 (t70) cc_final: 0.7423 (t0) REVERT: D 35 MET cc_start: 0.6879 (mpt) cc_final: 0.6018 (mpt) REVERT: D 36 ASN cc_start: 0.7609 (m110) cc_final: 0.7155 (m110) REVERT: D 66 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6872 (pmt) REVERT: D 79 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7500 (tpp) REVERT: D 101 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: D 180 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7282 (mp) REVERT: D 271 GLU cc_start: 0.7838 (mp0) cc_final: 0.7553 (mt-10) REVERT: E 36 ASN cc_start: 0.7838 (m110) cc_final: 0.7314 (m-40) REVERT: E 79 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7502 (tpp) REVERT: E 85 GLU cc_start: 0.7846 (mp0) cc_final: 0.7634 (mp0) REVERT: E 101 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6324 (mm-30) REVERT: E 128 MET cc_start: 0.9225 (ttm) cc_final: 0.8911 (ttp) REVERT: E 192 ASP cc_start: 0.8466 (t70) cc_final: 0.8117 (t0) REVERT: E 271 GLU cc_start: 0.7847 (mp0) cc_final: 0.7580 (mt-10) REVERT: F 36 ASN cc_start: 0.7929 (m110) cc_final: 0.7485 (m110) REVERT: F 192 ASP cc_start: 0.8378 (t70) cc_final: 0.8142 (t0) REVERT: G 66 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6804 (pmm) REVERT: G 192 ASP cc_start: 0.8411 (t70) cc_final: 0.8018 (t0) REVERT: H 36 ASN cc_start: 0.7836 (m110) cc_final: 0.7353 (m110) REVERT: H 66 MET cc_start: 0.7331 (pmm) cc_final: 0.6739 (pmm) REVERT: H 180 ILE cc_start: 0.7571 (mp) cc_final: 0.7361 (mp) REVERT: H 271 GLU cc_start: 0.7981 (mp0) cc_final: 0.7739 (mt-10) REVERT: H 281 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8041 (tttp) REVERT: I 66 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7185 (pmt) REVERT: I 266 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8674 (mttt) REVERT: J 38 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5730 (ttm-80) REVERT: J 48 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8372 (mt) REVERT: J 266 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8715 (mttt) REVERT: J 281 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8040 (tttp) REVERT: K 31 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.6185 (m-70) REVERT: K 76 ASP cc_start: 0.7859 (t70) cc_final: 0.7452 (m-30) REVERT: K 247 ASP cc_start: 0.7975 (t70) cc_final: 0.7459 (t0) REVERT: K 271 GLU cc_start: 0.7981 (mp0) cc_final: 0.7706 (mt-10) REVERT: L 36 ASN cc_start: 0.7656 (m110) cc_final: 0.7226 (m110) REVERT: L 101 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6295 (mm-30) REVERT: L 122 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7989 (tmtt) REVERT: L 192 ASP cc_start: 0.8404 (t70) cc_final: 0.8023 (t0) REVERT: L 271 GLU cc_start: 0.7914 (mp0) cc_final: 0.7595 (mm-30) REVERT: L 325 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5018 (mpt) outliers start: 54 outliers final: 10 residues processed: 492 average time/residue: 0.7303 time to fit residues: 416.4391 Evaluate side-chains 466 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 437 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 79 MET Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 128 MET Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 92 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 242 GLN D 161 ASN F 242 GLN G 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.164844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123319 restraints weight = 33466.981| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.87 r_work: 0.3244 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29244 Z= 0.111 Angle : 0.487 9.402 39360 Z= 0.257 Chirality : 0.043 0.145 4452 Planarity : 0.003 0.039 5076 Dihedral : 4.234 52.353 4008 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.49 % Allowed : 13.46 % Favored : 85.05 % 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: 1.87 (0.14), residues: 3672 helix: 1.69 (0.11), residues: 2244 sheet: 1.38 (0.24), residues: 492 loop : 0.21 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 297 TYR 0.012 0.001 TYR A 241 PHE 0.010 0.001 PHE E 288 TRP 0.008 0.002 TRP C 328 HIS 0.006 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00257 (29244) covalent geometry : angle 0.48717 (39360) hydrogen bonds : bond 0.03888 ( 1701) hydrogen bonds : angle 4.19397 ( 4947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 454 time to evaluate : 1.333 Fit side-chains REVERT: A 128 MET cc_start: 0.9069 (ttp) cc_final: 0.8747 (ttp) REVERT: B 35 MET cc_start: 0.6755 (mpt) cc_final: 0.6540 (mpt) REVERT: B 66 MET cc_start: 0.7566 (pmm) cc_final: 0.7018 (pmm) REVERT: B 274 LYS cc_start: 0.8437 (mptt) cc_final: 0.8095 (mtmt) REVERT: C 36 ASN cc_start: 0.7732 (m-40) cc_final: 0.7245 (m110) REVERT: C 101 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6397 (mm-30) REVERT: C 250 TYR cc_start: 0.8058 (t80) cc_final: 0.7430 (m-10) REVERT: D 36 ASN cc_start: 0.7409 (m110) cc_final: 0.6950 (m110) REVERT: D 48 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8299 (mt) REVERT: D 101 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6417 (mm-30) REVERT: E 36 ASN cc_start: 0.7711 (m110) cc_final: 0.7193 (m-40) REVERT: E 76 ASP cc_start: 0.7629 (t70) cc_final: 0.6967 (t0) REVERT: E 101 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6264 (mm-30) REVERT: E 128 MET cc_start: 0.9163 (ttm) cc_final: 0.8909 (ttp) REVERT: E 192 ASP cc_start: 0.8304 (t70) cc_final: 0.7937 (t0) REVERT: F 36 ASN cc_start: 0.7888 (m110) cc_final: 0.7420 (m110) REVERT: F 192 ASP cc_start: 0.8302 (t70) cc_final: 0.8068 (t0) REVERT: G 35 MET cc_start: 0.7033 (mmm) cc_final: 0.6604 (mpm) REVERT: G 66 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6860 (pmm) REVERT: G 192 ASP cc_start: 0.8227 (t70) cc_final: 0.7778 (t0) REVERT: G 242 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7733 (mp-120) REVERT: G 250 TYR cc_start: 0.7911 (t80) cc_final: 0.7417 (m-10) REVERT: H 31 HIS cc_start: 0.6614 (t-170) cc_final: 0.6236 (t70) REVERT: H 36 ASN cc_start: 0.7575 (m110) cc_final: 0.7104 (m110) REVERT: H 66 MET cc_start: 0.7511 (pmm) cc_final: 0.6862 (pmm) REVERT: I 35 MET cc_start: 0.6885 (mmt) cc_final: 0.6536 (mpt) REVERT: I 266 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8521 (mttt) REVERT: J 48 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (mt) REVERT: J 266 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8530 (mttt) REVERT: K 31 HIS cc_start: 0.6212 (OUTLIER) cc_final: 0.5997 (m-70) REVERT: K 35 MET cc_start: 0.7001 (mpt) cc_final: 0.6745 (mmt) REVERT: K 66 MET cc_start: 0.7362 (pmt) cc_final: 0.6783 (pmm) REVERT: L 6 TYR cc_start: 0.7960 (m-80) cc_final: 0.7616 (m-80) REVERT: L 31 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.5783 (m170) REVERT: L 36 ASN cc_start: 0.7535 (m110) cc_final: 0.7101 (m110) REVERT: L 122 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7952 (tmtt) REVERT: L 192 ASP cc_start: 0.8165 (t70) cc_final: 0.7793 (t0) REVERT: L 250 TYR cc_start: 0.8140 (t80) cc_final: 0.7500 (m-10) REVERT: L 325 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5061 (mpt) outliers start: 45 outliers final: 8 residues processed: 475 average time/residue: 0.7134 time to fit residues: 394.4281 Evaluate side-chains 480 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 460 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 242 GLN Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 308 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 136 optimal weight: 10.0000 chunk 352 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN D 161 ASN F 242 GLN G 242 GLN H 31 HIS I 242 GLN J 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121731 restraints weight = 33665.887| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.11 r_work: 0.3247 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29244 Z= 0.107 Angle : 0.487 9.715 39360 Z= 0.256 Chirality : 0.043 0.173 4452 Planarity : 0.003 0.037 5076 Dihedral : 4.123 52.139 4008 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.09 % Allowed : 13.99 % Favored : 84.92 % 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: 2.09 (0.14), residues: 3672 helix: 1.88 (0.11), residues: 2232 sheet: 1.46 (0.24), residues: 492 loop : 0.27 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 297 TYR 0.013 0.001 TYR L 241 PHE 0.010 0.001 PHE E 288 TRP 0.008 0.001 TRP E 328 HIS 0.007 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00246 (29244) covalent geometry : angle 0.48698 (39360) hydrogen bonds : bond 0.03836 ( 1701) hydrogen bonds : angle 4.15357 ( 4947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 467 time to evaluate : 1.150 Fit side-chains REVERT: A 94 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 128 MET cc_start: 0.9063 (ttp) cc_final: 0.8749 (ttp) REVERT: B 35 MET cc_start: 0.6790 (mpt) cc_final: 0.5862 (mpt) REVERT: B 66 MET cc_start: 0.7599 (pmm) cc_final: 0.7038 (pmm) REVERT: B 274 LYS cc_start: 0.8442 (mptt) cc_final: 0.8109 (mtmt) REVERT: C 36 ASN cc_start: 0.7713 (m-40) cc_final: 0.7242 (m110) REVERT: C 101 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6344 (mm-30) REVERT: C 250 TYR cc_start: 0.8075 (t80) cc_final: 0.7424 (m-10) REVERT: D 36 ASN cc_start: 0.7399 (m110) cc_final: 0.6918 (m110) REVERT: D 48 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8306 (mt) REVERT: D 101 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6381 (mm-30) REVERT: D 180 ILE cc_start: 0.7631 (mp) cc_final: 0.7418 (mp) REVERT: E 36 ASN cc_start: 0.7687 (m110) cc_final: 0.7172 (m-40) REVERT: E 128 MET cc_start: 0.9163 (ttm) cc_final: 0.8890 (ttp) REVERT: E 192 ASP cc_start: 0.8332 (t70) cc_final: 0.7980 (t0) REVERT: F 36 ASN cc_start: 0.7909 (m110) cc_final: 0.7451 (m110) REVERT: F 192 ASP cc_start: 0.8286 (t70) cc_final: 0.8040 (t0) REVERT: F 247 ASP cc_start: 0.7791 (t70) cc_final: 0.7441 (t70) REVERT: G 35 MET cc_start: 0.7036 (mmm) cc_final: 0.6665 (mpm) REVERT: G 66 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6870 (pmm) REVERT: G 192 ASP cc_start: 0.8235 (t70) cc_final: 0.7827 (t0) REVERT: G 247 ASP cc_start: 0.7703 (t70) cc_final: 0.7219 (t0) REVERT: G 250 TYR cc_start: 0.7943 (t80) cc_final: 0.7424 (m-10) REVERT: H 36 ASN cc_start: 0.7548 (m110) cc_final: 0.7092 (m110) REVERT: H 66 MET cc_start: 0.7546 (pmm) cc_final: 0.6883 (pmm) REVERT: I 266 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (mttt) REVERT: J 48 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8390 (mt) REVERT: K 31 HIS cc_start: 0.6135 (OUTLIER) cc_final: 0.5912 (m-70) REVERT: K 66 MET cc_start: 0.7249 (pmt) cc_final: 0.6705 (pmm) REVERT: K 76 ASP cc_start: 0.7710 (t70) cc_final: 0.7117 (t0) REVERT: L 6 TYR cc_start: 0.7965 (m-80) cc_final: 0.7751 (m-80) REVERT: L 31 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5844 (m170) REVERT: L 35 MET cc_start: 0.6988 (mpt) cc_final: 0.6698 (mpt) REVERT: L 36 ASN cc_start: 0.7410 (m110) cc_final: 0.6999 (m110) REVERT: L 66 MET cc_start: 0.7377 (pmt) cc_final: 0.6987 (pmm) REVERT: L 101 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6016 (mm-30) REVERT: L 122 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7958 (tmtt) REVERT: L 192 ASP cc_start: 0.8182 (t70) cc_final: 0.7798 (t0) REVERT: L 250 TYR cc_start: 0.8151 (t80) cc_final: 0.7514 (m-10) REVERT: L 325 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5138 (mpt) outliers start: 33 outliers final: 13 residues processed: 485 average time/residue: 0.6961 time to fit residues: 393.3047 Evaluate side-chains 477 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 454 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 242 GLN Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 201 optimal weight: 6.9990 chunk 131 optimal weight: 0.0000 chunk 371 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 335 optimal weight: 3.9990 chunk 337 optimal weight: 0.8980 chunk 342 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 242 GLN B 161 ASN B 197 GLN B 242 GLN C 209 GLN D 161 ASN F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118883 restraints weight = 33540.876| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.89 r_work: 0.3224 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29244 Z= 0.140 Angle : 0.529 11.424 39360 Z= 0.276 Chirality : 0.044 0.155 4452 Planarity : 0.003 0.037 5076 Dihedral : 4.197 48.662 4008 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.22 % Allowed : 14.15 % Favored : 84.62 % 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: 1.96 (0.14), residues: 3672 helix: 1.77 (0.11), residues: 2232 sheet: 1.40 (0.24), residues: 492 loop : 0.23 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 297 TYR 0.015 0.001 TYR L 241 PHE 0.012 0.002 PHE E 288 TRP 0.009 0.002 TRP D 328 HIS 0.008 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00339 (29244) covalent geometry : angle 0.52874 (39360) hydrogen bonds : bond 0.04588 ( 1701) hydrogen bonds : angle 4.19960 ( 4947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 454 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 128 MET cc_start: 0.9105 (ttp) cc_final: 0.8753 (ttp) REVERT: B 66 MET cc_start: 0.7518 (pmm) cc_final: 0.6980 (pmm) REVERT: B 274 LYS cc_start: 0.8407 (mptt) cc_final: 0.8060 (mtmt) REVERT: C 36 ASN cc_start: 0.7724 (m-40) cc_final: 0.7245 (m110) REVERT: C 101 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6354 (mm-30) REVERT: C 271 GLU cc_start: 0.7731 (mp0) cc_final: 0.7462 (mt-10) REVERT: D 36 ASN cc_start: 0.7506 (m110) cc_final: 0.7045 (m110) REVERT: D 48 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (mt) REVERT: D 66 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6885 (pmt) REVERT: D 101 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: D 180 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7384 (mp) REVERT: E 36 ASN cc_start: 0.7665 (m110) cc_final: 0.7145 (m-40) REVERT: E 128 MET cc_start: 0.9199 (ttm) cc_final: 0.8892 (ttp) REVERT: E 192 ASP cc_start: 0.8347 (t70) cc_final: 0.7977 (t0) REVERT: F 36 ASN cc_start: 0.7914 (m110) cc_final: 0.7451 (m110) REVERT: F 192 ASP cc_start: 0.8275 (t70) cc_final: 0.8025 (t0) REVERT: F 247 ASP cc_start: 0.7768 (t70) cc_final: 0.7374 (t70) REVERT: F 271 GLU cc_start: 0.7814 (mp0) cc_final: 0.7451 (mt-10) REVERT: G 35 MET cc_start: 0.6943 (mmm) cc_final: 0.6226 (mpm) REVERT: G 66 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6898 (pmm) REVERT: G 192 ASP cc_start: 0.8231 (t70) cc_final: 0.7820 (t0) REVERT: H 36 ASN cc_start: 0.7560 (m110) cc_final: 0.7114 (m110) REVERT: H 66 MET cc_start: 0.7431 (pmm) cc_final: 0.6760 (pmm) REVERT: I 35 MET cc_start: 0.6825 (mmt) cc_final: 0.6341 (mpt) REVERT: I 76 ASP cc_start: 0.7860 (t70) cc_final: 0.7312 (m-30) REVERT: I 247 ASP cc_start: 0.7900 (t70) cc_final: 0.7384 (t0) REVERT: I 266 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8552 (mttt) REVERT: J 48 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8338 (mt) REVERT: K 31 HIS cc_start: 0.6206 (OUTLIER) cc_final: 0.5912 (m-70) REVERT: K 271 GLU cc_start: 0.7795 (mp0) cc_final: 0.7488 (mt-10) REVERT: L 6 TYR cc_start: 0.7930 (m-80) cc_final: 0.7590 (m-80) REVERT: L 31 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5818 (m170) REVERT: L 35 MET cc_start: 0.6853 (mpt) cc_final: 0.6649 (mpt) REVERT: L 36 ASN cc_start: 0.7431 (m110) cc_final: 0.6983 (m110) REVERT: L 101 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6029 (mm-30) REVERT: L 122 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7961 (tmtt) REVERT: L 192 ASP cc_start: 0.8188 (t70) cc_final: 0.7831 (t0) REVERT: L 250 TYR cc_start: 0.8121 (t80) cc_final: 0.7464 (m-10) REVERT: L 325 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5061 (mpt) outliers start: 37 outliers final: 15 residues processed: 473 average time/residue: 0.6973 time to fit residues: 384.0639 Evaluate side-chains 459 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 432 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 242 GLN Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 82 optimal weight: 0.7980 chunk 365 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 255 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 242 GLN B 161 ASN B 197 GLN B 242 GLN D 31 HIS D 161 ASN F 242 GLN G 242 GLN I 242 GLN J 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128839 restraints weight = 33243.696| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.97 r_work: 0.3360 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29244 Z= 0.118 Angle : 0.514 10.989 39360 Z= 0.268 Chirality : 0.043 0.153 4452 Planarity : 0.003 0.037 5076 Dihedral : 4.146 50.611 4008 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.03 % Allowed : 14.58 % Favored : 84.39 % 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: 2.06 (0.14), residues: 3672 helix: 1.85 (0.11), residues: 2232 sheet: 1.42 (0.24), residues: 492 loop : 0.28 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 297 TYR 0.014 0.001 TYR B 241 PHE 0.010 0.001 PHE E 288 TRP 0.008 0.002 TRP D 328 HIS 0.009 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00276 (29244) covalent geometry : angle 0.51393 (39360) hydrogen bonds : bond 0.04056 ( 1701) hydrogen bonds : angle 4.16971 ( 4947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 459 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7151 (pmt) cc_final: 0.6898 (pmm) REVERT: A 94 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 128 MET cc_start: 0.8997 (ttp) cc_final: 0.8719 (ttp) REVERT: B 66 MET cc_start: 0.7586 (pmm) cc_final: 0.7098 (pmm) REVERT: B 274 LYS cc_start: 0.8546 (mptt) cc_final: 0.8346 (mtmt) REVERT: C 36 ASN cc_start: 0.7758 (m-40) cc_final: 0.7331 (m110) REVERT: C 48 LEU cc_start: 0.8612 (mp) cc_final: 0.8392 (mm) REVERT: C 101 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6372 (mm-30) REVERT: D 36 ASN cc_start: 0.7614 (m110) cc_final: 0.7180 (m110) REVERT: D 48 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8350 (mt) REVERT: D 66 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6996 (pmt) REVERT: D 101 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6312 (mm-30) REVERT: E 36 ASN cc_start: 0.7793 (m110) cc_final: 0.7310 (m-40) REVERT: E 128 MET cc_start: 0.9065 (ttm) cc_final: 0.8793 (ttp) REVERT: E 192 ASP cc_start: 0.8308 (t70) cc_final: 0.8046 (t0) REVERT: F 36 ASN cc_start: 0.8011 (m110) cc_final: 0.7598 (m110) REVERT: G 35 MET cc_start: 0.7087 (mmm) cc_final: 0.6712 (mpm) REVERT: G 66 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7016 (pmm) REVERT: G 192 ASP cc_start: 0.8234 (t70) cc_final: 0.7941 (t0) REVERT: G 242 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8259 (mm110) REVERT: G 247 ASP cc_start: 0.7779 (t70) cc_final: 0.7342 (t0) REVERT: G 250 TYR cc_start: 0.7893 (t80) cc_final: 0.7556 (m-10) REVERT: H 66 MET cc_start: 0.7532 (pmm) cc_final: 0.6897 (pmm) REVERT: I 35 MET cc_start: 0.6988 (mmt) cc_final: 0.6671 (mpt) REVERT: I 266 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8615 (mttt) REVERT: J 48 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8313 (mp) REVERT: K 31 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5737 (m-70) REVERT: K 66 MET cc_start: 0.7328 (pmt) cc_final: 0.6902 (pmm) REVERT: K 76 ASP cc_start: 0.7666 (t70) cc_final: 0.7131 (t0) REVERT: L 6 TYR cc_start: 0.8078 (m-80) cc_final: 0.7738 (m-80) REVERT: L 36 ASN cc_start: 0.7583 (m110) cc_final: 0.7166 (m110) REVERT: L 66 MET cc_start: 0.7352 (pmt) cc_final: 0.7000 (pmm) REVERT: L 101 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5959 (mm-30) REVERT: L 122 LYS cc_start: 0.8292 (mmmt) cc_final: 0.8043 (tmtt) REVERT: L 192 ASP cc_start: 0.8172 (t70) cc_final: 0.7892 (t0) REVERT: L 250 TYR cc_start: 0.8145 (t80) cc_final: 0.7673 (m-10) REVERT: L 325 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5225 (mpt) outliers start: 31 outliers final: 11 residues processed: 474 average time/residue: 0.7164 time to fit residues: 394.5811 Evaluate side-chains 469 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 447 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 317 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 240 optimal weight: 0.0870 chunk 265 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 242 GLN B 161 ASN B 197 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN H 242 GLN I 242 GLN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128973 restraints weight = 33489.314| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.01 r_work: 0.3355 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.250 29244 Z= 0.181 Angle : 0.698 59.195 39360 Z= 0.392 Chirality : 0.043 0.164 4452 Planarity : 0.004 0.159 5076 Dihedral : 4.147 50.656 4008 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.96 % Allowed : 14.75 % Favored : 84.29 % Cbeta Deviations : 0.06 % 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: 2.05 (0.14), residues: 3672 helix: 1.84 (0.11), residues: 2232 sheet: 1.42 (0.24), residues: 492 loop : 0.28 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 297 TYR 0.013 0.001 TYR B 241 PHE 0.013 0.001 PHE L 26 TRP 0.008 0.002 TRP D 328 HIS 0.009 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00398 (29244) covalent geometry : angle 0.69761 (39360) hydrogen bonds : bond 0.04131 ( 1701) hydrogen bonds : angle 4.17371 ( 4947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11145.09 seconds wall clock time: 190 minutes 24.28 seconds (11424.28 seconds total)