Starting phenix.real_space_refine on Sat Jun 21 19:00:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i22_35129/06_2025/8i22_35129_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i22_35129/06_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_35129/06_2025/8i22_35129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i22_35129/06_2025/8i22_35129.map" model { file = "/net/cci-nas-00/data/ceres_data/8i22_35129/06_2025/8i22_35129_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i22_35129/06_2025/8i22_35129_neut.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.02, per 1000 atoms: 0.55 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: 5.81 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 3.19 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: 9.56 Time building geometry restraints manager: 6.94 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 55.600 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (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 TRP 0.008 0.001 TRP E 290 HIS 0.011 0.001 HIS C 45 PHE 0.011 0.001 PHE B 225 TYR 0.011 0.001 TYR E 245 ARG 0.004 0.000 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.17699 ( 930) hydrogen bonds : angle 7.19015 ( 2574) covalent geometry : bond 0.00655 (25962) covalent geometry : angle 0.71679 (35196) *********************** 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 : 2.744 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: 1.5705 time to fit residues: 580.8164 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 : 2.861 ------------------------------------------------------------------------------- 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 268 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 D 260 GLN E 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.167709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096706 restraints weight = 23648.160| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.72 r_work: 0.3104 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 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 = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 25962 Z= 0.162 Angle : 0.584 7.505 35196 Z= 0.310 Chirality : 0.047 0.149 3978 Planarity : 0.004 0.037 4488 Dihedral : 6.633 73.155 3504 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.41 % Favored : 96.21 % Rotamer: Outliers : 1.66 % Allowed : 15.55 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3168 helix: 0.94 (0.16), residues: 1086 sheet: 0.18 (0.22), residues: 510 loop : -0.85 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 402 HIS 0.005 0.001 HIS B 74 PHE 0.013 0.002 PHE D 225 TYR 0.014 0.001 TYR A 245 ARG 0.003 0.000 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 930) hydrogen bonds : angle 5.67222 ( 2574) covalent geometry : bond 0.00363 (25962) covalent geometry : angle 0.58405 (35196) *********************** 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 325 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 3.347 Fit side-chains REVERT: A 113 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8537 (mt) REVERT: A 256 ASN cc_start: 0.8597 (t0) cc_final: 0.8267 (t0) REVERT: A 288 SER cc_start: 0.7982 (m) cc_final: 0.7706 (p) REVERT: A 430 MET cc_start: 0.7399 (tpt) cc_final: 0.7131 (tpt) REVERT: F 113 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (mt) REVERT: F 197 MET cc_start: 0.8759 (mmp) cc_final: 0.7979 (mtp) REVERT: F 344 GLN cc_start: 0.8254 (pt0) cc_final: 0.8013 (pt0) REVERT: B 113 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 288 SER cc_start: 0.7996 (m) cc_final: 0.7733 (p) REVERT: C 113 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 197 MET cc_start: 0.8754 (mmp) cc_final: 0.7973 (mtp) REVERT: C 344 GLN cc_start: 0.8253 (pt0) cc_final: 0.8013 (pt0) REVERT: D 113 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8561 (mt) REVERT: D 288 SER cc_start: 0.8240 (m) cc_final: 0.7788 (p) REVERT: E 113 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (mt) REVERT: E 288 SER cc_start: 0.8242 (m) cc_final: 0.7791 (p) REVERT: E 428 LYS cc_start: 0.8465 (mttm) cc_final: 0.8088 (mmtt) outliers start: 46 outliers final: 2 residues processed: 323 average time/residue: 1.5739 time to fit residues: 579.7205 Evaluate side-chains 264 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 256 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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 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 247 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 135 optimal weight: 0.3980 chunk 181 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 260 GLN E 344 GLN E 395 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099656 restraints weight = 23752.093| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.71 r_work: 0.3144 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 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 = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1450 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= 0.105 Angle : 0.522 7.097 35196 Z= 0.276 Chirality : 0.045 0.140 3978 Planarity : 0.004 0.034 4488 Dihedral : 6.259 78.897 3492 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.91 % Favored : 95.71 % Rotamer: Outliers : 1.37 % Allowed : 16.52 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3168 helix: 1.12 (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 TRP 0.007 0.001 TRP F 402 HIS 0.003 0.001 HIS A 74 PHE 0.011 0.001 PHE E 225 TYR 0.010 0.001 TYR A 245 ARG 0.002 0.000 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 930) hydrogen bonds : angle 5.27152 ( 2574) covalent geometry : bond 0.00230 (25962) covalent geometry : angle 0.52248 (35196) *********************** 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 315 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 3.140 Fit side-chains REVERT: A 113 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 256 ASN cc_start: 0.8610 (t0) cc_final: 0.8289 (t0) REVERT: A 288 SER cc_start: 0.7898 (m) cc_final: 0.7646 (p) REVERT: A 428 LYS cc_start: 0.8496 (mttm) cc_final: 0.8180 (mmtm) REVERT: A 430 MET cc_start: 0.7366 (tpt) cc_final: 0.7131 (tpt) REVERT: F 113 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8369 (mt) REVERT: F 288 SER cc_start: 0.8164 (m) cc_final: 0.7875 (p) REVERT: F 344 GLN cc_start: 0.8147 (pt0) cc_final: 0.7882 (pt0) REVERT: B 113 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 288 SER cc_start: 0.7905 (m) cc_final: 0.7662 (p) REVERT: B 428 LYS cc_start: 0.8497 (mttm) cc_final: 0.8182 (mmtm) REVERT: B 430 MET cc_start: 0.7370 (tpt) cc_final: 0.7141 (tpt) REVERT: C 113 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 288 SER cc_start: 0.8162 (m) cc_final: 0.7873 (p) REVERT: C 344 GLN cc_start: 0.8150 (pt0) cc_final: 0.7887 (pt0) REVERT: D 113 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8254 (mt) REVERT: D 232 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8394 (mm) REVERT: D 288 SER cc_start: 0.8048 (m) cc_final: 0.7640 (p) REVERT: E 113 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8250 (mt) REVERT: E 232 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8394 (mm) REVERT: E 288 SER cc_start: 0.8053 (m) cc_final: 0.7649 (p) REVERT: E 428 LYS cc_start: 0.8517 (mttm) cc_final: 0.8121 (mmtt) outliers start: 38 outliers final: 4 residues processed: 311 average time/residue: 1.5397 time to fit residues: 547.6730 Evaluate side-chains 275 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 263 time to evaluate : 3.167 ------------------------------------------------------------------------------- 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 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 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 226 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 316 optimal weight: 0.0020 chunk 74 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 262 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.170288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101953 restraints weight = 24008.737| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.99 r_work: 0.3148 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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 = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25962 Z= 0.099 Angle : 0.501 7.164 35196 Z= 0.264 Chirality : 0.044 0.141 3978 Planarity : 0.003 0.032 4488 Dihedral : 6.158 85.172 3492 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.57 % Favored : 96.05 % Rotamer: Outliers : 1.37 % Allowed : 17.03 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3168 helix: 1.32 (0.16), residues: 1086 sheet: 0.39 (0.23), residues: 510 loop : -0.71 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 402 HIS 0.003 0.001 HIS A 74 PHE 0.012 0.001 PHE B 225 TYR 0.009 0.001 TYR A 245 ARG 0.002 0.000 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 930) hydrogen bonds : angle 5.05408 ( 2574) covalent geometry : bond 0.00218 (25962) covalent geometry : angle 0.50102 (35196) *********************** 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 318 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 2.760 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: 0.8549 (OUTLIER) cc_final: 0.8246 (mt) REVERT: A 256 ASN cc_start: 0.8637 (t0) cc_final: 0.8308 (t0) REVERT: A 288 SER cc_start: 0.7869 (m) cc_final: 0.7620 (p) REVERT: A 428 LYS cc_start: 0.8500 (mttm) cc_final: 0.8184 (mmtm) REVERT: F 61 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8522 (mtmm) REVERT: F 113 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8329 (mt) REVERT: F 288 SER cc_start: 0.8137 (m) cc_final: 0.7859 (p) REVERT: F 331 GLN cc_start: 0.7698 (mm110) cc_final: 0.6896 (mt0) REVERT: B 113 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 288 SER cc_start: 0.7874 (m) cc_final: 0.7631 (p) REVERT: B 428 LYS cc_start: 0.8500 (mttm) cc_final: 0.8174 (mmtm) REVERT: C 61 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8510 (mtmm) REVERT: C 113 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8328 (mt) REVERT: C 288 SER cc_start: 0.8146 (m) cc_final: 0.7869 (p) REVERT: C 331 GLN cc_start: 0.7699 (mm110) cc_final: 0.6898 (mt0) REVERT: D 113 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8237 (mt) REVERT: D 232 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8321 (mm) REVERT: D 281 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7619 (ttpt) REVERT: D 288 SER cc_start: 0.7979 (m) cc_final: 0.7609 (p) REVERT: D 428 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8120 (mmtp) REVERT: E 113 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8234 (mt) REVERT: E 232 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8320 (mm) REVERT: E 281 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7614 (ttpt) REVERT: E 288 SER cc_start: 0.7986 (m) cc_final: 0.7621 (p) REVERT: E 428 LYS cc_start: 0.8492 (mttm) cc_final: 0.8094 (mmtt) outliers start: 38 outliers final: 14 residues processed: 312 average time/residue: 1.5059 time to fit residues: 540.5642 Evaluate side-chains 296 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 2.853 ------------------------------------------------------------------------------- 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 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 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 232 LEU Chi-restraints excluded: chain E residue 285 MET 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 75 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 317 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.168828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100025 restraints weight = 23877.519| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.02 r_work: 0.3116 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 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 = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1709 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= 0.121 Angle : 0.519 7.241 35196 Z= 0.274 Chirality : 0.045 0.146 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.302 87.929 3492 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 1.52 % Allowed : 16.78 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3168 helix: 1.31 (0.16), residues: 1086 sheet: 0.35 (0.22), residues: 510 loop : -0.66 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 402 HIS 0.003 0.001 HIS F 39 PHE 0.013 0.001 PHE B 225 TYR 0.011 0.001 TYR A 245 ARG 0.002 0.000 ARG E 211 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 930) hydrogen bonds : angle 5.12463 ( 2574) covalent geometry : bond 0.00269 (25962) covalent geometry : angle 0.51894 (35196) *********************** 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 323 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 5.195 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: 0.8713 (OUTLIER) cc_final: 0.8364 (mt) REVERT: A 256 ASN cc_start: 0.8646 (t0) cc_final: 0.8319 (t0) REVERT: A 288 SER cc_start: 0.7862 (m) cc_final: 0.7602 (p) REVERT: A 428 LYS cc_start: 0.8550 (mttm) cc_final: 0.8226 (mmtm) REVERT: F 61 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8588 (mtmm) REVERT: F 113 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8446 (mt) REVERT: F 288 SER cc_start: 0.7912 (m) cc_final: 0.7641 (p) REVERT: F 331 GLN cc_start: 0.7630 (mm110) cc_final: 0.6863 (mt0) REVERT: B 113 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 288 SER cc_start: 0.7865 (m) cc_final: 0.7606 (p) REVERT: B 428 LYS cc_start: 0.8520 (mttm) cc_final: 0.8182 (mmtm) REVERT: C 61 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8574 (mtmm) REVERT: C 113 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8436 (mt) REVERT: C 288 SER cc_start: 0.7918 (m) cc_final: 0.7651 (p) REVERT: C 331 GLN cc_start: 0.7626 (mm110) cc_final: 0.6859 (mt0) REVERT: D 113 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8364 (mt) REVERT: D 232 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 281 LYS cc_start: 0.8427 (ttpt) cc_final: 0.7627 (ttpt) REVERT: D 288 SER cc_start: 0.7977 (m) cc_final: 0.7629 (p) REVERT: D 428 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8098 (mmtp) REVERT: E 113 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8358 (mt) REVERT: E 232 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8390 (mm) REVERT: E 281 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7615 (ttpt) REVERT: E 288 SER cc_start: 0.7985 (m) cc_final: 0.7642 (p) REVERT: E 428 LYS cc_start: 0.8497 (mttm) cc_final: 0.8079 (mmtt) outliers start: 42 outliers final: 16 residues processed: 319 average time/residue: 1.7052 time to fit residues: 625.2503 Evaluate side-chains 297 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 3.624 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 44 optimal weight: 40.0000 chunk 217 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 263 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.168432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100473 restraints weight = 23698.705| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.03 r_work: 0.3103 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 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 = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25962 Z= 0.125 Angle : 0.521 7.243 35196 Z= 0.275 Chirality : 0.045 0.145 3978 Planarity : 0.004 0.031 4488 Dihedral : 6.316 89.085 3492 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.50 % Favored : 96.12 % Rotamer: Outliers : 1.34 % Allowed : 16.70 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3168 helix: 1.30 (0.16), residues: 1086 sheet: 0.32 (0.22), residues: 510 loop : -0.64 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 402 HIS 0.003 0.001 HIS F 39 PHE 0.013 0.001 PHE B 225 TYR 0.012 0.001 TYR A 245 ARG 0.002 0.000 ARG E 211 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 930) hydrogen bonds : angle 5.12221 ( 2574) covalent geometry : bond 0.00280 (25962) covalent geometry : angle 0.52068 (35196) *********************** 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 312 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 2.914 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: 0.8750 (OUTLIER) cc_final: 0.8395 (mt) REVERT: A 256 ASN cc_start: 0.8649 (t0) cc_final: 0.8315 (t0) REVERT: A 288 SER cc_start: 0.7866 (m) cc_final: 0.7604 (p) REVERT: A 428 LYS cc_start: 0.8599 (mttm) cc_final: 0.8303 (mmtm) REVERT: F 61 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8610 (mtmm) REVERT: F 113 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8481 (mt) REVERT: F 288 SER cc_start: 0.7901 (m) cc_final: 0.7623 (p) REVERT: F 331 GLN cc_start: 0.7583 (mm110) cc_final: 0.6859 (mt0) REVERT: B 113 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 256 ASN cc_start: 0.8565 (t0) cc_final: 0.8218 (t0) REVERT: B 288 SER cc_start: 0.7871 (m) cc_final: 0.7610 (p) REVERT: B 428 LYS cc_start: 0.8572 (mttm) cc_final: 0.8255 (mmtm) REVERT: C 61 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8600 (mtmm) REVERT: C 113 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8481 (mt) REVERT: C 288 SER cc_start: 0.7899 (m) cc_final: 0.7625 (p) REVERT: C 331 GLN cc_start: 0.7579 (mm110) cc_final: 0.6857 (mt0) REVERT: D 113 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8403 (mt) REVERT: D 232 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8392 (mm) REVERT: D 281 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7611 (ttpt) REVERT: D 288 SER cc_start: 0.7962 (m) cc_final: 0.7622 (p) REVERT: D 428 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8141 (mmtp) REVERT: E 113 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8396 (mt) REVERT: E 232 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8391 (mm) REVERT: E 281 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7606 (ttpt) REVERT: E 288 SER cc_start: 0.7970 (m) cc_final: 0.7633 (p) REVERT: E 428 LYS cc_start: 0.8610 (mttm) cc_final: 0.8173 (mmtt) outliers start: 37 outliers final: 17 residues processed: 309 average time/residue: 1.4192 time to fit residues: 504.9577 Evaluate side-chains 294 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 2.776 ------------------------------------------------------------------------------- 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 197 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 59 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 237 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 254 optimal weight: 0.0870 chunk 114 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.170489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105441 restraints weight = 23843.508| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.15 r_work: 0.3130 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 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 = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25962 Z= 0.091 Angle : 0.487 7.018 35196 Z= 0.256 Chirality : 0.044 0.137 3978 Planarity : 0.003 0.031 4488 Dihedral : 6.096 88.401 3492 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.72 % Favored : 95.90 % Rotamer: Outliers : 1.23 % Allowed : 16.99 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3168 helix: 1.42 (0.16), residues: 1086 sheet: 0.32 (0.22), residues: 510 loop : -0.58 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS C 39 PHE 0.011 0.001 PHE E 225 TYR 0.008 0.001 TYR B 245 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 930) hydrogen bonds : angle 4.88238 ( 2574) covalent geometry : bond 0.00202 (25962) covalent geometry : angle 0.48721 (35196) *********************** 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 301 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 3.614 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: 0.8540 (OUTLIER) cc_final: 0.8244 (mt) REVERT: A 256 ASN cc_start: 0.8656 (t0) cc_final: 0.8345 (t0) REVERT: A 288 SER cc_start: 0.7816 (m) cc_final: 0.7539 (p) REVERT: A 428 LYS cc_start: 0.8575 (mttm) cc_final: 0.8289 (mmtm) REVERT: F 61 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8600 (mtmm) REVERT: F 113 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8294 (mt) REVERT: F 288 SER cc_start: 0.7923 (m) cc_final: 0.7662 (p) REVERT: F 331 GLN cc_start: 0.7552 (mm110) cc_final: 0.6847 (mt0) REVERT: B 113 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 256 ASN cc_start: 0.8584 (t0) cc_final: 0.8227 (t0) REVERT: B 288 SER cc_start: 0.7811 (m) cc_final: 0.7532 (p) REVERT: B 428 LYS cc_start: 0.8543 (mttm) cc_final: 0.8224 (mmtm) REVERT: B 430 MET cc_start: 0.7537 (mmm) cc_final: 0.7294 (tpt) REVERT: C 61 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8582 (mtmm) REVERT: C 113 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8291 (mt) REVERT: C 288 SER cc_start: 0.7921 (m) cc_final: 0.7664 (p) REVERT: C 331 GLN cc_start: 0.7553 (mm110) cc_final: 0.6851 (mt0) REVERT: D 113 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8244 (mt) REVERT: D 232 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8267 (mm) REVERT: D 281 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7580 (ttpt) REVERT: D 288 SER cc_start: 0.7901 (m) cc_final: 0.7588 (p) REVERT: D 428 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8131 (mmtp) REVERT: E 113 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8237 (mt) REVERT: E 232 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8297 (mm) REVERT: E 281 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7575 (ttpt) REVERT: E 288 SER cc_start: 0.7905 (m) cc_final: 0.7600 (p) REVERT: E 428 LYS cc_start: 0.8597 (mttm) cc_final: 0.8158 (mmtt) REVERT: E 430 MET cc_start: 0.7335 (tpt) cc_final: 0.7093 (tpt) outliers start: 34 outliers final: 16 residues processed: 297 average time/residue: 1.6723 time to fit residues: 575.4301 Evaluate side-chains 291 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 2.848 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 193 optimal weight: 6.9990 chunk 212 optimal weight: 0.0270 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 302 optimal weight: 9.9990 chunk 43 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 232 optimal weight: 0.2980 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 214 GLN C 214 GLN C 390 ASN D 344 GLN E 344 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.166355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097442 restraints weight = 23657.313| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.08 r_work: 0.3066 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25962 Z= 0.200 Angle : 0.586 11.017 35196 Z= 0.309 Chirality : 0.049 0.161 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.558 88.838 3492 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.35 % Favored : 96.28 % Rotamer: Outliers : 1.05 % Allowed : 17.14 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3168 helix: 1.17 (0.16), residues: 1086 sheet: 0.30 (0.22), residues: 510 loop : -0.61 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 402 HIS 0.005 0.001 HIS C 195 PHE 0.015 0.002 PHE E 225 TYR 0.018 0.002 TYR B 245 ARG 0.005 0.001 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 930) hydrogen bonds : angle 5.39491 ( 2574) covalent geometry : bond 0.00457 (25962) covalent geometry : angle 0.58646 (35196) *********************** 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 300 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 3.317 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: 0.8969 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 256 ASN cc_start: 0.8679 (t0) cc_final: 0.8343 (t0) REVERT: A 288 SER cc_start: 0.7914 (m) cc_final: 0.7664 (p) REVERT: A 428 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (mmtm) REVERT: F 61 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8649 (mtmm) REVERT: F 113 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8710 (mt) REVERT: F 288 SER cc_start: 0.8017 (m) cc_final: 0.7733 (p) REVERT: B 113 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8698 (mt) REVERT: B 288 SER cc_start: 0.7919 (m) cc_final: 0.7673 (p) REVERT: C 61 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8641 (mtmm) REVERT: C 113 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8715 (mt) REVERT: C 288 SER cc_start: 0.8012 (m) cc_final: 0.7727 (p) REVERT: C 331 GLN cc_start: 0.7587 (mm110) cc_final: 0.6881 (mt0) REVERT: C 344 GLN cc_start: 0.8140 (pt0) cc_final: 0.7856 (pt0) REVERT: D 113 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8740 (mt) REVERT: D 232 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8492 (mm) REVERT: D 288 SER cc_start: 0.8100 (m) cc_final: 0.7714 (p) REVERT: E 113 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8730 (mt) REVERT: E 232 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8490 (mm) REVERT: E 288 SER cc_start: 0.8091 (m) cc_final: 0.7719 (p) outliers start: 29 outliers final: 10 residues processed: 297 average time/residue: 1.9132 time to fit residues: 651.6566 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 : 4.357 ------------------------------------------------------------------------------- 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 113 ILE Chi-restraints excluded: chain C residue 463 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 143 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 310 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 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 = 0.4050 r_free = 0.4050 target = 0.168325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100430 restraints weight = 23839.114| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.08 r_work: 0.3108 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25962 Z= 0.119 Angle : 0.519 8.643 35196 Z= 0.273 Chirality : 0.045 0.145 3978 Planarity : 0.004 0.031 4488 Dihedral : 6.318 89.921 3492 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.82 % Favored : 95.80 % Rotamer: Outliers : 0.98 % Allowed : 17.39 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3168 helix: 1.26 (0.16), residues: 1086 sheet: 0.24 (0.22), residues: 510 loop : -0.59 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 402 HIS 0.003 0.001 HIS D 39 PHE 0.013 0.001 PHE E 225 TYR 0.011 0.001 TYR B 245 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 930) hydrogen bonds : angle 5.09741 ( 2574) covalent geometry : bond 0.00268 (25962) covalent geometry : angle 0.51883 (35196) *********************** 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 295 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 2.975 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: 0.8735 (OUTLIER) cc_final: 0.8390 (mt) REVERT: A 256 ASN cc_start: 0.8661 (t0) cc_final: 0.8313 (t0) REVERT: A 288 SER cc_start: 0.7862 (m) cc_final: 0.7614 (p) REVERT: A 428 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8299 (mmtm) REVERT: F 61 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8628 (mtmm) REVERT: F 113 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8465 (mt) REVERT: F 288 SER cc_start: 0.7900 (m) cc_final: 0.7639 (p) REVERT: B 113 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8385 (mt) REVERT: B 256 ASN cc_start: 0.8589 (t0) cc_final: 0.8214 (t0) REVERT: B 288 SER cc_start: 0.7872 (m) cc_final: 0.7621 (p) REVERT: B 428 LYS cc_start: 0.8544 (mttm) cc_final: 0.8228 (mmtm) REVERT: C 61 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8618 (mtmm) REVERT: C 113 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8464 (mt) REVERT: C 288 SER cc_start: 0.7901 (m) cc_final: 0.7646 (p) REVERT: C 331 GLN cc_start: 0.7571 (mm110) cc_final: 0.6870 (mt0) REVERT: D 113 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8465 (mt) REVERT: D 154 GLN cc_start: 0.7740 (pt0) cc_final: 0.7468 (mm110) REVERT: D 232 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8364 (mm) REVERT: D 281 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7597 (ttpt) REVERT: D 288 SER cc_start: 0.7980 (m) cc_final: 0.7660 (p) REVERT: D 428 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8158 (mmtm) REVERT: E 113 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8463 (mt) REVERT: E 154 GLN cc_start: 0.7749 (pt0) cc_final: 0.7470 (mm110) REVERT: E 232 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8365 (mm) REVERT: E 281 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7591 (ttpt) REVERT: E 288 SER cc_start: 0.7978 (m) cc_final: 0.7668 (p) outliers start: 27 outliers final: 12 residues processed: 292 average time/residue: 1.4769 time to fit residues: 497.5759 Evaluate side-chains 292 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 269 time to evaluate : 2.978 ------------------------------------------------------------------------------- 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 113 ILE 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 132 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.0000 chunk 136 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 276 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.167302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098634 restraints weight = 23714.157| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.96 r_work: 0.3098 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25962 Z= 0.150 Angle : 0.548 11.150 35196 Z= 0.288 Chirality : 0.046 0.152 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.407 89.994 3492 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.28 % Favored : 96.34 % Rotamer: Outliers : 0.83 % Allowed : 17.46 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3168 helix: 1.21 (0.16), residues: 1086 sheet: 0.22 (0.22), residues: 510 loop : -0.57 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 402 HIS 0.003 0.001 HIS D 39 PHE 0.015 0.002 PHE D 225 TYR 0.015 0.001 TYR B 245 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 930) hydrogen bonds : angle 5.21890 ( 2574) covalent geometry : bond 0.00341 (25962) covalent geometry : angle 0.54767 (35196) ********************** 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 288 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 2.834 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: 0.8841 (OUTLIER) cc_final: 0.8496 (mt) REVERT: A 238 MET cc_start: 0.8810 (tpt) cc_final: 0.6902 (tpt) REVERT: A 256 ASN cc_start: 0.8671 (t0) cc_final: 0.8339 (t0) REVERT: A 288 SER cc_start: 0.7905 (m) cc_final: 0.7681 (p) REVERT: F 61 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8611 (mtmm) REVERT: F 113 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (mt) REVERT: F 288 SER cc_start: 0.7928 (m) cc_final: 0.7662 (p) REVERT: B 113 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8491 (mt) REVERT: B 238 MET cc_start: 0.8809 (tpt) cc_final: 0.6899 (tpt) REVERT: B 288 SER cc_start: 0.7901 (m) cc_final: 0.7682 (p) REVERT: B 428 LYS cc_start: 0.8556 (mttm) cc_final: 0.8269 (mmtm) REVERT: C 61 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: C 113 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8597 (mt) REVERT: C 288 SER cc_start: 0.7927 (m) cc_final: 0.7664 (p) REVERT: C 344 GLN cc_start: 0.8112 (pt0) cc_final: 0.7844 (pt0) REVERT: D 113 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8611 (mt) REVERT: D 154 GLN cc_start: 0.7747 (pt0) cc_final: 0.7494 (mm110) REVERT: D 232 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8418 (mm) REVERT: D 281 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7598 (ttpt) REVERT: D 288 SER cc_start: 0.8019 (m) cc_final: 0.7683 (p) REVERT: E 113 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (mt) REVERT: E 154 GLN cc_start: 0.7762 (pt0) cc_final: 0.7501 (mm110) REVERT: E 232 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 281 LYS cc_start: 0.8456 (ttpt) cc_final: 0.7595 (ttpt) REVERT: E 288 SER cc_start: 0.8018 (m) cc_final: 0.7688 (p) outliers start: 23 outliers final: 12 residues processed: 287 average time/residue: 1.4770 time to fit residues: 485.8832 Evaluate side-chains 284 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 3.006 ------------------------------------------------------------------------------- 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 113 ILE 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 135 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 0.0010 chunk 311 optimal weight: 30.0000 chunk 151 optimal weight: 30.0000 chunk 114 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.168851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103441 restraints weight = 23766.991| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.15 r_work: 0.3097 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 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 = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2021 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 9.011 35196 Z= 0.267 Chirality : 0.045 0.141 3978 Planarity : 0.003 0.032 4488 Dihedral : 6.240 89.739 3492 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.76 % Favored : 95.86 % Rotamer: Outliers : 1.05 % Allowed : 17.25 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3168 helix: 1.30 (0.16), residues: 1086 sheet: 0.21 (0.22), residues: 510 loop : -0.53 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 402 HIS 0.003 0.001 HIS E 39 PHE 0.013 0.001 PHE D 225 TYR 0.010 0.001 TYR A 245 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 930) hydrogen bonds : angle 5.01067 ( 2574) covalent geometry : bond 0.00239 (25962) covalent geometry : angle 0.50853 (35196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32953.99 seconds wall clock time: 573 minutes 8.37 seconds (34388.37 seconds total)