Starting phenix.real_space_refine on Mon Aug 25 04:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i22_35129/08_2025/8i22_35129_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i22_35129/08_2025/8i22_35129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i22_35129/08_2025/8i22_35129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i22_35129/08_2025/8i22_35129.map" model { file = "/net/cci-nas-00/data/ceres_data/8i22_35129/08_2025/8i22_35129_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i22_35129/08_2025/8i22_35129_neut.cif" } resolution = 2.15 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= 0.001 sd= 0.066 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 108 5.16 5 C 16296 2.51 5 N 4236 2.21 5 O 4758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25398 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.66, per 1000 atoms: 0.18 Number of scatterers: 25398 At special positions: 0 Unit cell: (173.91, 158.1, 92.07, 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 108 16.00 O 4758 8.00 N 4236 7.00 C 16296 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: 1.52 Conformation dependent library (CDL) restraints added in 881.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 30 sheets defined 38.5% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.600A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.636A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.775A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 321 through 324 removed outlier: 4.399A pdb=" N GLY A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.558A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.718A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.540A pdb=" N ASP A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.698A pdb=" N LEU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 removed outlier: 3.599A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.636A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.775A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 283 Processing helix chain 'F' and resid 300 through 310 Processing helix chain 'F' and resid 321 through 324 removed outlier: 4.399A pdb=" N GLY F 324 " --> pdb=" O SER F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 340 through 349 removed outlier: 3.557A pdb=" N GLU F 346 " --> pdb=" O ASP F 342 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.718A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 441 through 448 removed outlier: 3.540A pdb=" N ASP F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 493 removed outlier: 3.699A pdb=" N LEU F 487 " --> pdb=" O THR F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.600A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.635A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.774A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 321 through 324 removed outlier: 4.399A pdb=" N GLY B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.558A pdb=" N GLU B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.718A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.539A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.698A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 removed outlier: 3.600A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.636A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.775A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 321 through 324 removed outlier: 4.399A pdb=" N GLY C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'C' and resid 340 through 349 removed outlier: 3.558A pdb=" N GLU C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.718A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 441 through 448 removed outlier: 3.540A pdb=" N ASP C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.698A pdb=" N LEU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.599A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.636A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.776A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 321 through 324 removed outlier: 4.399A pdb=" N GLY D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 340 through 349 removed outlier: 3.559A pdb=" N GLU D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.718A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 441 through 448 removed outlier: 3.540A pdb=" N ASP D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 493 removed outlier: 3.698A pdb=" N LEU D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 removed outlier: 3.600A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.635A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.776A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 283 Processing helix chain 'E' and resid 300 through 310 Processing helix chain 'E' and resid 321 through 324 removed outlier: 4.399A pdb=" N GLY E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 340 through 349 removed outlier: 3.558A pdb=" N GLU E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR E 347 " --> pdb=" O GLN E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.718A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 441 through 448 removed outlier: 3.539A pdb=" N ASP E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.699A pdb=" N LEU E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.711A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 292 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY A 317 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE A 294 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.510A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 5.236A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 425 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 433 Processing sheet with id=AA5, first strand: chain 'A' and resid 457 through 461 removed outlier: 8.331A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.710A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 292 " --> pdb=" O PHE F 315 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY F 317 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE F 294 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.510A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 359 through 363 removed outlier: 5.236A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 425 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 430 through 433 Processing sheet with id=AB1, first strand: chain 'F' and resid 457 through 461 removed outlier: 8.331A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.710A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 292 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY B 317 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE B 294 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.510A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 359 through 363 removed outlier: 5.236A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 425 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 430 through 433 Processing sheet with id=AB6, first strand: chain 'B' and resid 457 through 461 removed outlier: 8.331A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.710A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 292 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY C 317 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 294 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.510A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 363 removed outlier: 5.236A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 425 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 430 through 433 Processing sheet with id=AC2, first strand: chain 'C' and resid 457 through 461 removed outlier: 8.331A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.711A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 292 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY D 317 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE D 294 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.510A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.235A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 425 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 430 through 433 Processing sheet with id=AC7, first strand: chain 'D' and resid 457 through 461 removed outlier: 8.331A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.711A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL E 292 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY E 317 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE E 294 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLY E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.510A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 359 through 363 removed outlier: 5.236A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 425 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 430 through 433 Processing sheet with id=AD3, first strand: chain 'E' and resid 457 through 461 removed outlier: 8.331A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2574 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: 4.81 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4296 1.27 - 1.41: 6253 1.41 - 1.54: 14894 1.54 - 1.67: 327 1.67 - 1.80: 192 Bond restraints: 25962 Sorted by residual: bond pdb=" CA THR F 175 " pdb=" C THR F 175 " ideal model delta sigma weight residual 1.522 1.410 0.112 1.20e-02 6.94e+03 8.66e+01 bond pdb=" CA THR A 175 " pdb=" C THR A 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.63e+01 bond pdb=" CA THR B 175 " pdb=" C THR B 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.59e+01 bond pdb=" CA THR D 175 " pdb=" C THR D 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.56e+01 bond pdb=" CA THR E 175 " pdb=" C THR E 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.56e+01 ... (remaining 25957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 34460 2.14 - 4.28: 598 4.28 - 6.42: 84 6.42 - 8.56: 30 8.56 - 10.70: 24 Bond angle restraints: 35196 Sorted by residual: angle pdb=" N PRO A 470 " pdb=" CA PRO A 470 " pdb=" C PRO A 470 " ideal model delta sigma weight residual 110.21 120.31 -10.10 1.64e+00 3.72e-01 3.79e+01 angle pdb=" N PRO D 470 " pdb=" CA PRO D 470 " pdb=" C PRO D 470 " ideal model delta sigma weight residual 110.21 120.30 -10.09 1.64e+00 3.72e-01 3.78e+01 angle pdb=" N PRO F 470 " pdb=" CA PRO F 470 " pdb=" C PRO F 470 " ideal model delta sigma weight residual 110.21 120.29 -10.08 1.64e+00 3.72e-01 3.78e+01 angle pdb=" N PRO E 470 " pdb=" CA PRO E 470 " pdb=" C PRO E 470 " ideal model delta sigma weight residual 110.21 120.28 -10.07 1.64e+00 3.72e-01 3.77e+01 angle pdb=" N PRO B 470 " pdb=" CA PRO B 470 " pdb=" C PRO B 470 " ideal model delta sigma weight residual 110.21 120.26 -10.05 1.64e+00 3.72e-01 3.75e+01 ... (remaining 35191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 13432 17.41 - 34.82: 1459 34.82 - 52.23: 505 52.23 - 69.64: 138 69.64 - 87.05: 54 Dihedral angle restraints: 15588 sinusoidal: 6318 harmonic: 9270 Sorted by residual: dihedral pdb=" CA PRO F 325 " pdb=" C PRO F 325 " pdb=" N ILE F 326 " pdb=" CA ILE F 326 " ideal model delta harmonic sigma weight residual -180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO B 325 " pdb=" C PRO B 325 " pdb=" N ILE B 326 " pdb=" CA ILE B 326 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO A 325 " pdb=" C PRO A 325 " pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 15585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3482 0.082 - 0.164: 428 0.164 - 0.246: 38 0.246 - 0.328: 18 0.328 - 0.409: 12 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA LYS D 396 " pdb=" N LYS D 396 " pdb=" C LYS D 396 " pdb=" CB LYS D 396 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA LYS F 396 " pdb=" N LYS F 396 " pdb=" C LYS F 396 " pdb=" CB LYS F 396 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LYS A 396 " pdb=" N LYS A 396 " pdb=" C LYS A 396 " pdb=" CB LYS A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 3975 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 532 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C HIS B 532 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS B 532 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 533 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 532 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C HIS C 532 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 532 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU C 533 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 532 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C HIS A 532 " -0.047 2.00e-02 2.50e+03 pdb=" O HIS A 532 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 533 " 0.016 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4405 2.77 - 3.30: 23930 3.30 - 3.83: 46775 3.83 - 4.37: 58161 4.37 - 4.90: 92056 Nonbonded interactions: 225327 Sorted by model distance: nonbonded pdb=" OG1 THR B 518 " pdb=" O LYS B 522 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR C 518 " pdb=" O LYS C 522 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 518 " pdb=" O LYS A 522 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR F 518 " pdb=" O LYS F 522 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR D 518 " pdb=" O LYS D 522 " model vdw 2.237 3.040 ... (remaining 225322 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.00 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: 2.850 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.920 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.007 0.129 25962 Z= 0.433 Angle : 0.717 10.703 35196 Z= 0.418 Chirality : 0.058 0.409 3978 Planarity : 0.005 0.051 4488 Dihedral : 17.835 87.050 9624 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % Rotamer: Outliers : 0.65 % Allowed : 17.35 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.28 (0.14), residues: 3168 helix: 0.73 (0.16), residues: 1080 sheet: 0.14 (0.22), residues: 522 loop : -0.92 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 96 TYR 0.011 0.001 TYR E 245 PHE 0.011 0.001 PHE B 225 TRP 0.008 0.001 TRP E 290 HIS 0.011 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00655 (25962) covalent geometry : angle 0.71679 (35196) hydrogen bonds : bond 0.17699 ( 930) hydrogen bonds : angle 7.19015 ( 2574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 308 time to evaluate : 1.065 Fit side-chains REVERT: F 197 MET cc_start: 0.8637 (mmp) cc_final: 0.8126 (mtp) REVERT: C 197 MET cc_start: 0.8636 (mmp) cc_final: 0.8124 (mtp) outliers start: 18 outliers final: 9 residues processed: 326 average time/residue: 0.6626 time to fit residues: 244.3237 Evaluate side-chains 261 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 2.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN F 390 ASN B 260 GLN C 390 ASN D 260 GLN E 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098664 restraints weight = 23774.878| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.00 r_work: 0.3098 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25962 Z= 0.157 Angle : 0.580 7.560 35196 Z= 0.309 Chirality : 0.047 0.150 3978 Planarity : 0.004 0.038 4488 Dihedral : 6.627 73.986 3504 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.35 % Favored : 96.28 % Rotamer: Outliers : 1.84 % Allowed : 15.26 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.08 (0.15), residues: 3168 helix: 0.96 (0.16), residues: 1086 sheet: 0.19 (0.22), residues: 510 loop : -0.83 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 47 TYR 0.014 0.001 TYR A 245 PHE 0.014 0.002 PHE D 225 TRP 0.011 0.002 TRP C 402 HIS 0.004 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00350 (25962) covalent geometry : angle 0.57998 (35196) hydrogen bonds : bond 0.04341 ( 930) hydrogen bonds : angle 5.63242 ( 2574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 0.914 Fit side-chains REVERT: A 113 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8492 (mt) REVERT: A 256 ASN cc_start: 0.8603 (t0) cc_final: 0.8276 (t0) REVERT: A 288 SER cc_start: 0.7968 (m) cc_final: 0.7682 (p) REVERT: A 428 LYS cc_start: 0.8462 (mttm) cc_final: 0.8160 (mmtm) REVERT: F 113 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8573 (mt) REVERT: F 197 MET cc_start: 0.8774 (mmp) cc_final: 0.7984 (mtp) REVERT: F 344 GLN cc_start: 0.8242 (pt0) cc_final: 0.7992 (pt0) REVERT: B 113 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 256 ASN cc_start: 0.8586 (t0) cc_final: 0.8260 (t0) REVERT: B 288 SER cc_start: 0.7984 (m) cc_final: 0.7715 (p) REVERT: C 113 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 197 MET cc_start: 0.8767 (mmp) cc_final: 0.7979 (mtp) REVERT: C 344 GLN cc_start: 0.8246 (pt0) cc_final: 0.7999 (pt0) REVERT: D 113 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 288 SER cc_start: 0.8232 (m) cc_final: 0.7775 (p) REVERT: E 113 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8552 (mt) REVERT: E 288 SER cc_start: 0.8234 (m) cc_final: 0.7779 (p) outliers start: 51 outliers final: 3 residues processed: 329 average time/residue: 0.6577 time to fit residues: 246.0582 Evaluate side-chains 267 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 258 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 15 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN C 154 GLN D 344 GLN D 395 ASN E 344 GLN E 395 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.169544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.099415 restraints weight = 23925.893| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.70 r_work: 0.3139 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25962 Z= 0.109 Angle : 0.525 7.148 35196 Z= 0.277 Chirality : 0.045 0.142 3978 Planarity : 0.004 0.034 4488 Dihedral : 6.284 80.124 3492 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 1.30 % Allowed : 16.85 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.10 (0.15), residues: 3168 helix: 1.14 (0.16), residues: 1092 sheet: 0.38 (0.23), residues: 510 loop : -0.79 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 47 TYR 0.010 0.001 TYR A 245 PHE 0.011 0.001 PHE D 225 TRP 0.008 0.001 TRP F 402 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00240 (25962) covalent geometry : angle 0.52477 (35196) hydrogen bonds : bond 0.03677 ( 930) hydrogen bonds : angle 5.27573 ( 2574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 1.139 Fit side-chains REVERT: A 113 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 256 ASN cc_start: 0.8616 (t0) cc_final: 0.8297 (t0) REVERT: A 288 SER cc_start: 0.7894 (m) cc_final: 0.7646 (p) REVERT: A 428 LYS cc_start: 0.8503 (mttm) cc_final: 0.8189 (mmtm) REVERT: F 61 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8507 (mtmm) REVERT: F 113 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8382 (mt) REVERT: F 288 SER cc_start: 0.8083 (m) cc_final: 0.7816 (p) REVERT: F 344 GLN cc_start: 0.8143 (pt0) cc_final: 0.7878 (pt0) REVERT: B 113 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 256 ASN cc_start: 0.8624 (t0) cc_final: 0.8312 (t0) REVERT: B 288 SER cc_start: 0.7895 (m) cc_final: 0.7655 (p) REVERT: B 428 LYS cc_start: 0.8492 (mttm) cc_final: 0.8175 (mmtm) REVERT: C 61 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8506 (mtmm) REVERT: C 113 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8380 (mt) REVERT: C 288 SER cc_start: 0.8075 (m) cc_final: 0.7805 (p) REVERT: C 344 GLN cc_start: 0.8145 (pt0) cc_final: 0.7883 (pt0) REVERT: D 113 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8285 (mt) REVERT: D 232 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8407 (mm) REVERT: D 288 SER cc_start: 0.8021 (m) cc_final: 0.7619 (p) REVERT: E 113 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8280 (mt) REVERT: E 232 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8406 (mm) REVERT: E 288 SER cc_start: 0.8025 (m) cc_final: 0.7624 (p) REVERT: E 428 LYS cc_start: 0.8517 (mttm) cc_final: 0.8126 (mmtt) outliers start: 36 outliers final: 4 residues processed: 304 average time/residue: 0.7733 time to fit residues: 267.2810 Evaluate side-chains 281 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 267 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 136 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 287 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN E 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.167620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096946 restraints weight = 23666.079| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.69 r_work: 0.3100 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25962 Z= 0.151 Angle : 0.546 7.419 35196 Z= 0.290 Chirality : 0.046 0.149 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.392 82.452 3492 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.35 % Favored : 96.28 % Rotamer: Outliers : 1.16 % Allowed : 16.67 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.13 (0.15), residues: 3168 helix: 1.14 (0.16), residues: 1086 sheet: 0.35 (0.22), residues: 510 loop : -0.72 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 211 TYR 0.014 0.001 TYR A 245 PHE 0.014 0.002 PHE D 225 TRP 0.010 0.001 TRP C 402 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00342 (25962) covalent geometry : angle 0.54634 (35196) hydrogen bonds : bond 0.04067 ( 930) hydrogen bonds : angle 5.34402 ( 2574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 256 ASN cc_start: 0.8628 (t0) cc_final: 0.8294 (t0) REVERT: A 288 SER cc_start: 0.7912 (m) cc_final: 0.7657 (p) REVERT: A 428 LYS cc_start: 0.8499 (mttm) cc_final: 0.8179 (mmtm) REVERT: F 61 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8557 (mtmm) REVERT: F 113 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8577 (mt) REVERT: F 288 SER cc_start: 0.8037 (m) cc_final: 0.7773 (p) REVERT: F 344 GLN cc_start: 0.8140 (pt0) cc_final: 0.7867 (pt0) REVERT: B 113 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8448 (mt) REVERT: B 256 ASN cc_start: 0.8632 (t0) cc_final: 0.8304 (t0) REVERT: B 288 SER cc_start: 0.7917 (m) cc_final: 0.7670 (p) REVERT: B 428 LYS cc_start: 0.8510 (mttm) cc_final: 0.8183 (mmtm) REVERT: B 430 MET cc_start: 0.7507 (mmm) cc_final: 0.7175 (tpt) REVERT: C 61 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8552 (mtmm) REVERT: C 113 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 232 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (mm) REVERT: C 288 SER cc_start: 0.8032 (m) cc_final: 0.7769 (p) REVERT: C 344 GLN cc_start: 0.8147 (pt0) cc_final: 0.7869 (pt0) REVERT: D 113 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8550 (mt) REVERT: D 232 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8483 (mm) REVERT: D 281 LYS cc_start: 0.8499 (ttpt) cc_final: 0.7639 (ttpt) REVERT: D 288 SER cc_start: 0.8105 (m) cc_final: 0.7711 (p) REVERT: D 428 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8119 (mmtp) REVERT: E 113 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8547 (mt) REVERT: E 232 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8482 (mm) REVERT: E 288 SER cc_start: 0.8110 (m) cc_final: 0.7718 (p) REVERT: E 428 LYS cc_start: 0.8521 (mttm) cc_final: 0.8110 (mmtt) outliers start: 32 outliers final: 7 residues processed: 308 average time/residue: 0.7608 time to fit residues: 267.0284 Evaluate side-chains 290 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 254 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 313 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN E 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.168356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099239 restraints weight = 23681.978| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.14 r_work: 0.3082 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25962 Z= 0.136 Angle : 0.532 7.328 35196 Z= 0.282 Chirality : 0.046 0.144 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.347 84.084 3492 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.91 % Favored : 95.71 % Rotamer: Outliers : 1.45 % Allowed : 16.02 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.16 (0.15), residues: 3168 helix: 1.18 (0.16), residues: 1086 sheet: 0.29 (0.22), residues: 510 loop : -0.69 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 47 TYR 0.013 0.001 TYR A 245 PHE 0.014 0.001 PHE B 225 TRP 0.010 0.001 TRP C 402 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00307 (25962) covalent geometry : angle 0.53209 (35196) hydrogen bonds : bond 0.03856 ( 930) hydrogen bonds : angle 5.23731 ( 2574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8413 (mt) REVERT: A 197 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8350 (mpm) REVERT: A 256 ASN cc_start: 0.8654 (t0) cc_final: 0.8315 (t0) REVERT: A 288 SER cc_start: 0.7895 (m) cc_final: 0.7637 (p) REVERT: A 428 LYS cc_start: 0.8565 (mttm) cc_final: 0.8243 (mmtm) REVERT: F 61 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8569 (mtmm) REVERT: F 113 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8525 (mt) REVERT: F 288 SER cc_start: 0.7941 (m) cc_final: 0.7669 (p) REVERT: F 331 GLN cc_start: 0.7590 (mm110) cc_final: 0.6854 (mt0) REVERT: B 113 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 256 ASN cc_start: 0.8634 (t0) cc_final: 0.8299 (t0) REVERT: B 288 SER cc_start: 0.7898 (m) cc_final: 0.7645 (p) REVERT: B 428 LYS cc_start: 0.8555 (mttm) cc_final: 0.8220 (mmtm) REVERT: B 430 MET cc_start: 0.7550 (mmm) cc_final: 0.7273 (tpt) REVERT: C 61 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8562 (mtmm) REVERT: C 113 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 232 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 288 SER cc_start: 0.7937 (m) cc_final: 0.7666 (p) REVERT: C 331 GLN cc_start: 0.7584 (mm110) cc_final: 0.6849 (mt0) REVERT: D 113 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8502 (mt) REVERT: D 232 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8469 (mm) REVERT: D 281 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7619 (ttpt) REVERT: D 288 SER cc_start: 0.8010 (m) cc_final: 0.7647 (p) REVERT: D 428 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8125 (mmtp) REVERT: E 113 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8498 (mt) REVERT: E 232 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8468 (mm) REVERT: E 281 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7619 (ttpt) REVERT: E 288 SER cc_start: 0.8011 (m) cc_final: 0.7647 (p) REVERT: E 428 LYS cc_start: 0.8546 (mttm) cc_final: 0.8117 (mmtt) outliers start: 40 outliers final: 14 residues processed: 317 average time/residue: 0.7421 time to fit residues: 268.8389 Evaluate side-chains 296 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 138 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 312 optimal weight: 9.9990 chunk 279 optimal weight: 0.4980 chunk 302 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 140 optimal weight: 0.0980 chunk 155 optimal weight: 0.0370 chunk 1 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 331 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103408 restraints weight = 23899.347| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.04 r_work: 0.3147 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25962 Z= 0.092 Angle : 0.490 7.078 35196 Z= 0.258 Chirality : 0.044 0.136 3978 Planarity : 0.003 0.032 4488 Dihedral : 6.137 87.971 3492 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.47 % Favored : 96.15 % Rotamer: Outliers : 1.19 % Allowed : 16.67 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.32 (0.15), residues: 3168 helix: 1.38 (0.16), residues: 1086 sheet: 0.30 (0.22), residues: 510 loop : -0.63 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.009 0.001 TYR E 245 PHE 0.011 0.001 PHE B 225 TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00203 (25962) covalent geometry : angle 0.48985 (35196) hydrogen bonds : bond 0.03197 ( 930) hydrogen bonds : angle 4.91972 ( 2574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (mt) REVERT: A 256 ASN cc_start: 0.8637 (t0) cc_final: 0.8319 (t0) REVERT: A 288 SER cc_start: 0.7831 (m) cc_final: 0.7573 (p) REVERT: A 428 LYS cc_start: 0.8526 (mttm) cc_final: 0.8205 (mmtm) REVERT: F 113 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8274 (mt) REVERT: F 288 SER cc_start: 0.7906 (m) cc_final: 0.7659 (p) REVERT: F 331 GLN cc_start: 0.7577 (mm110) cc_final: 0.6847 (mt0) REVERT: B 113 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8209 (mt) REVERT: B 256 ASN cc_start: 0.8631 (t0) cc_final: 0.8312 (t0) REVERT: B 288 SER cc_start: 0.7822 (m) cc_final: 0.7565 (p) REVERT: B 428 LYS cc_start: 0.8515 (mttm) cc_final: 0.8178 (mmtm) REVERT: C 113 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 288 SER cc_start: 0.7911 (m) cc_final: 0.7667 (p) REVERT: C 331 GLN cc_start: 0.7568 (mm110) cc_final: 0.6837 (mt0) REVERT: D 113 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8221 (mt) REVERT: D 232 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8294 (mm) REVERT: D 281 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7565 (ttpt) REVERT: D 288 SER cc_start: 0.7906 (m) cc_final: 0.7601 (p) REVERT: D 428 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8082 (mmtp) REVERT: E 113 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8211 (mt) REVERT: E 232 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8296 (mm) REVERT: E 252 ASP cc_start: 0.8488 (m-30) cc_final: 0.8164 (m-30) REVERT: E 281 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7563 (ttpt) REVERT: E 288 SER cc_start: 0.7909 (m) cc_final: 0.7609 (p) REVERT: E 428 LYS cc_start: 0.8563 (mttm) cc_final: 0.8129 (mmtt) outliers start: 33 outliers final: 14 residues processed: 307 average time/residue: 0.7146 time to fit residues: 251.6122 Evaluate side-chains 290 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 163 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 12 optimal weight: 0.0470 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 40.0000 chunk 93 optimal weight: 7.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 GLN E 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.167363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098664 restraints weight = 23644.441| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.96 r_work: 0.3094 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25962 Z= 0.156 Angle : 0.546 8.207 35196 Z= 0.289 Chirality : 0.046 0.150 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.402 87.134 3492 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.72 % Favored : 95.90 % Rotamer: Outliers : 1.16 % Allowed : 16.85 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.25 (0.15), residues: 3168 helix: 1.24 (0.16), residues: 1086 sheet: 0.31 (0.22), residues: 510 loop : -0.62 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 211 TYR 0.015 0.001 TYR B 245 PHE 0.014 0.002 PHE D 225 TRP 0.010 0.001 TRP C 402 HIS 0.003 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00353 (25962) covalent geometry : angle 0.54632 (35196) hydrogen bonds : bond 0.04009 ( 930) hydrogen bonds : angle 5.24367 ( 2574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 256 ASN cc_start: 0.8648 (t0) cc_final: 0.8307 (t0) REVERT: A 288 SER cc_start: 0.7884 (m) cc_final: 0.7630 (p) REVERT: A 428 LYS cc_start: 0.8590 (mttm) cc_final: 0.8283 (mmtm) REVERT: F 61 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8620 (mtmm) REVERT: F 113 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8555 (mt) REVERT: F 288 SER cc_start: 0.7900 (m) cc_final: 0.7630 (p) REVERT: F 331 GLN cc_start: 0.7565 (mm110) cc_final: 0.6832 (mt0) REVERT: B 113 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 256 ASN cc_start: 0.8647 (t0) cc_final: 0.8298 (t0) REVERT: B 288 SER cc_start: 0.7883 (m) cc_final: 0.7633 (p) REVERT: B 428 LYS cc_start: 0.8589 (mttm) cc_final: 0.8266 (mmtm) REVERT: C 61 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8612 (mtmm) REVERT: C 113 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8548 (mt) REVERT: C 288 SER cc_start: 0.7902 (m) cc_final: 0.7635 (p) REVERT: C 331 GLN cc_start: 0.7564 (mm110) cc_final: 0.6829 (mt0) REVERT: D 113 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8564 (mt) REVERT: D 232 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8434 (mm) REVERT: D 281 LYS cc_start: 0.8441 (ttpt) cc_final: 0.7629 (ttpt) REVERT: D 288 SER cc_start: 0.7994 (m) cc_final: 0.7653 (p) REVERT: D 428 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8201 (mmtp) REVERT: E 113 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8563 (mt) REVERT: E 232 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8434 (mm) REVERT: E 281 LYS cc_start: 0.8436 (ttpt) cc_final: 0.7624 (ttpt) REVERT: E 288 SER cc_start: 0.7995 (m) cc_final: 0.7658 (p) outliers start: 32 outliers final: 15 residues processed: 305 average time/residue: 0.7457 time to fit residues: 259.9307 Evaluate side-chains 293 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 GLN D 260 GLN D 344 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.166556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098630 restraints weight = 23702.305| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.91 r_work: 0.3078 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25962 Z= 0.175 Angle : 0.567 9.406 35196 Z= 0.300 Chirality : 0.047 0.156 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.450 84.947 3492 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.38 % Favored : 96.24 % Rotamer: Outliers : 1.23 % Allowed : 16.88 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.18 (0.15), residues: 3168 helix: 1.15 (0.16), residues: 1086 sheet: 0.22 (0.22), residues: 510 loop : -0.61 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.015 0.002 TYR B 245 PHE 0.016 0.002 PHE D 225 TRP 0.012 0.001 TRP F 402 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00397 (25962) covalent geometry : angle 0.56692 (35196) hydrogen bonds : bond 0.04221 ( 930) hydrogen bonds : angle 5.34918 ( 2574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 256 ASN cc_start: 0.8675 (t0) cc_final: 0.8330 (t0) REVERT: A 288 SER cc_start: 0.7922 (m) cc_final: 0.7694 (p) REVERT: A 428 LYS cc_start: 0.8546 (mttm) cc_final: 0.8239 (mmtm) REVERT: F 61 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8664 (mtmm) REVERT: F 113 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (mt) REVERT: F 288 SER cc_start: 0.7965 (m) cc_final: 0.7702 (p) REVERT: F 343 GLN cc_start: 0.8718 (mt0) cc_final: 0.8503 (mt0) REVERT: F 344 GLN cc_start: 0.8114 (pt0) cc_final: 0.7798 (pt0) REVERT: B 113 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 256 ASN cc_start: 0.8675 (t0) cc_final: 0.8331 (t0) REVERT: B 288 SER cc_start: 0.7927 (m) cc_final: 0.7702 (p) REVERT: B 428 LYS cc_start: 0.8556 (mttm) cc_final: 0.8265 (mmtm) REVERT: C 61 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8659 (mtmm) REVERT: C 288 SER cc_start: 0.7963 (m) cc_final: 0.7701 (p) REVERT: C 343 GLN cc_start: 0.8716 (mt0) cc_final: 0.8502 (mt0) REVERT: C 344 GLN cc_start: 0.8114 (pt0) cc_final: 0.7802 (pt0) REVERT: D 113 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8720 (mt) REVERT: D 232 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8440 (mm) REVERT: D 288 SER cc_start: 0.8103 (m) cc_final: 0.7733 (p) REVERT: E 113 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8715 (mt) REVERT: E 232 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8441 (mm) REVERT: E 288 SER cc_start: 0.8107 (m) cc_final: 0.7741 (p) outliers start: 34 outliers final: 12 residues processed: 302 average time/residue: 0.7447 time to fit residues: 257.3244 Evaluate side-chains 282 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 171 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 161 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 279 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN E 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.168727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100590 restraints weight = 23843.521| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.96 r_work: 0.3129 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25962 Z= 0.107 Angle : 0.509 8.024 35196 Z= 0.268 Chirality : 0.045 0.138 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.219 87.343 3492 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.88 % Favored : 95.74 % Rotamer: Outliers : 0.98 % Allowed : 17.46 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.28 (0.15), residues: 3168 helix: 1.28 (0.16), residues: 1086 sheet: 0.21 (0.22), residues: 510 loop : -0.57 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.010 0.001 TYR B 245 PHE 0.012 0.001 PHE D 225 TRP 0.009 0.001 TRP F 402 HIS 0.003 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00240 (25962) covalent geometry : angle 0.50910 (35196) hydrogen bonds : bond 0.03469 ( 930) hydrogen bonds : angle 5.04760 ( 2574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8359 (mt) REVERT: A 256 ASN cc_start: 0.8649 (t0) cc_final: 0.8303 (t0) REVERT: A 288 SER cc_start: 0.7851 (m) cc_final: 0.7609 (p) REVERT: A 428 LYS cc_start: 0.8524 (mttm) cc_final: 0.8227 (mmtm) REVERT: F 61 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8624 (mtmm) REVERT: F 113 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8402 (mt) REVERT: F 288 SER cc_start: 0.7879 (m) cc_final: 0.7638 (p) REVERT: B 113 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 256 ASN cc_start: 0.8647 (t0) cc_final: 0.8299 (t0) REVERT: B 288 SER cc_start: 0.7819 (m) cc_final: 0.7583 (p) REVERT: B 428 LYS cc_start: 0.8539 (mttm) cc_final: 0.8255 (mmtm) REVERT: C 61 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8622 (mtmm) REVERT: C 288 SER cc_start: 0.7882 (m) cc_final: 0.7645 (p) REVERT: D 113 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8433 (mt) REVERT: D 154 GLN cc_start: 0.7714 (pt0) cc_final: 0.7464 (mm110) REVERT: D 232 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8334 (mm) REVERT: D 281 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7577 (ttpt) REVERT: D 288 SER cc_start: 0.7955 (m) cc_final: 0.7649 (p) REVERT: D 428 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8074 (mmtp) REVERT: E 113 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8431 (mt) REVERT: E 154 GLN cc_start: 0.7698 (pt0) cc_final: 0.7454 (mm110) REVERT: E 232 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8331 (mm) REVERT: E 281 LYS cc_start: 0.8395 (ttpt) cc_final: 0.7580 (ttpt) REVERT: E 288 SER cc_start: 0.7957 (m) cc_final: 0.7659 (p) outliers start: 27 outliers final: 13 residues processed: 294 average time/residue: 0.7428 time to fit residues: 249.6916 Evaluate side-chains 286 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 45 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 141 optimal weight: 0.0370 chunk 314 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.166958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099662 restraints weight = 23708.793| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.93 r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25962 Z= 0.154 Angle : 0.552 11.419 35196 Z= 0.290 Chirality : 0.047 0.153 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.370 87.458 3492 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.31 % Favored : 96.31 % Rotamer: Outliers : 0.87 % Allowed : 17.46 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.22 (0.15), residues: 3168 helix: 1.20 (0.16), residues: 1086 sheet: 0.19 (0.22), residues: 510 loop : -0.57 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.015 0.001 TYR A 245 PHE 0.014 0.002 PHE E 225 TRP 0.010 0.001 TRP F 402 HIS 0.004 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00351 (25962) covalent geometry : angle 0.55203 (35196) hydrogen bonds : bond 0.03985 ( 930) hydrogen bonds : angle 5.23972 ( 2574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 238 MET cc_start: 0.8858 (tpt) cc_final: 0.7008 (tpt) REVERT: A 256 ASN cc_start: 0.8648 (t0) cc_final: 0.8288 (t0) REVERT: A 288 SER cc_start: 0.7896 (m) cc_final: 0.7662 (p) REVERT: A 428 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8250 (mmtm) REVERT: F 61 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8638 (mtmm) REVERT: F 113 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (mt) REVERT: F 288 SER cc_start: 0.7918 (m) cc_final: 0.7643 (p) REVERT: F 343 GLN cc_start: 0.8677 (mt0) cc_final: 0.8461 (mt0) REVERT: B 113 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 238 MET cc_start: 0.8852 (tpt) cc_final: 0.7078 (tpt) REVERT: B 256 ASN cc_start: 0.8646 (t0) cc_final: 0.8292 (t0) REVERT: B 288 SER cc_start: 0.7897 (m) cc_final: 0.7665 (p) REVERT: B 428 LYS cc_start: 0.8537 (mttm) cc_final: 0.8266 (mmtm) REVERT: C 61 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8600 (mtmm) REVERT: C 288 SER cc_start: 0.7928 (m) cc_final: 0.7658 (p) REVERT: C 343 GLN cc_start: 0.8675 (mt0) cc_final: 0.8461 (mt0) REVERT: D 113 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8646 (mt) REVERT: D 154 GLN cc_start: 0.7768 (pt0) cc_final: 0.7504 (mm110) REVERT: D 232 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8451 (mm) REVERT: D 281 LYS cc_start: 0.8433 (ttpt) cc_final: 0.7568 (ttpt) REVERT: D 288 SER cc_start: 0.8009 (m) cc_final: 0.7668 (p) REVERT: E 113 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8646 (mt) REVERT: E 232 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8450 (mm) REVERT: E 281 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7580 (ttpt) REVERT: E 288 SER cc_start: 0.8014 (m) cc_final: 0.7678 (p) outliers start: 24 outliers final: 12 residues processed: 289 average time/residue: 0.7597 time to fit residues: 251.6600 Evaluate side-chains 287 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 290 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 229 optimal weight: 0.5980 chunk 240 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.168572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101173 restraints weight = 23649.255| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.04 r_work: 0.3107 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25962 Z= 0.110 Angle : 0.512 9.281 35196 Z= 0.269 Chirality : 0.045 0.140 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.227 89.498 3492 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.72 % Favored : 95.90 % Rotamer: Outliers : 1.05 % Allowed : 17.21 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.29 (0.15), residues: 3168 helix: 1.28 (0.16), residues: 1086 sheet: 0.18 (0.22), residues: 522 loop : -0.53 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.011 0.001 TYR A 245 PHE 0.013 0.001 PHE D 225 TRP 0.008 0.001 TRP F 402 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00249 (25962) covalent geometry : angle 0.51221 (35196) hydrogen bonds : bond 0.03475 ( 930) hydrogen bonds : angle 5.03097 ( 2574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14009.79 seconds wall clock time: 238 minutes 46.85 seconds (14326.85 seconds total)