Starting phenix.real_space_refine on Sat May 24 06:10:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i22_35129/05_2025/8i22_35129_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i22_35129/05_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_35129/05_2025/8i22_35129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i22_35129/05_2025/8i22_35129.map" model { file = "/net/cci-nas-00/data/ceres_data/8i22_35129/05_2025/8i22_35129_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i22_35129/05_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-5687/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: 14.65, per 1000 atoms: 0.58 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: 6.87 Conformation dependent library (CDL) restraints added in 3.2 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: 3.69 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: 9.74 Time building geometry restraints manager: 7.87 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 58.160 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.860 ------------------------------------------------------------------------------- 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 : 2.647 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: 1.5112 time to fit residues: 560.4161 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 : 2.711 ------------------------------------------------------------------------------- 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 = 73)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096678 restraints weight = 23648.166| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.72 r_work: 0.3101 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 0.58406 (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 : 2.589 Fit side-chains REVERT: A 113 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8538 (mt) REVERT: A 256 ASN cc_start: 0.8593 (t0) cc_final: 0.8261 (t0) REVERT: A 288 SER cc_start: 0.7977 (m) cc_final: 0.7698 (p) REVERT: A 430 MET cc_start: 0.7403 (tpt) cc_final: 0.7135 (tpt) REVERT: F 113 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 197 MET cc_start: 0.8760 (mmp) cc_final: 0.7976 (mtp) REVERT: F 344 GLN cc_start: 0.8247 (pt0) cc_final: 0.8005 (pt0) REVERT: B 113 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8531 (mt) REVERT: B 288 SER cc_start: 0.7989 (m) cc_final: 0.7723 (p) REVERT: C 113 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8576 (mt) REVERT: C 197 MET cc_start: 0.8754 (mmp) cc_final: 0.7970 (mtp) REVERT: C 344 GLN cc_start: 0.8250 (pt0) cc_final: 0.8010 (pt0) REVERT: D 113 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8560 (mt) REVERT: D 288 SER cc_start: 0.8235 (m) cc_final: 0.7781 (p) REVERT: E 113 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8560 (mt) REVERT: E 288 SER cc_start: 0.8239 (m) cc_final: 0.7785 (p) REVERT: E 428 LYS cc_start: 0.8466 (mttm) cc_final: 0.8088 (mmtt) outliers start: 46 outliers final: 2 residues processed: 323 average time/residue: 1.4990 time to fit residues: 553.4873 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 : 2.608 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 174 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 188 optimal weight: 0.2980 chunk 135 optimal weight: 0.4980 chunk 181 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN C 154 GLN D 344 GLN D 395 ASN E 344 GLN E 395 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100033 restraints weight = 23761.140| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.70 r_work: 0.3147 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 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 = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1463 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= 0.104 Angle : 0.520 7.065 35196 Z= 0.274 Chirality : 0.044 0.140 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.243 79.343 3492 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.23 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: 0.11 (0.15), residues: 3168 helix: 1.14 (0.16), residues: 1092 sheet: 0.39 (0.23), residues: 510 loop : -0.78 (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 0.03585 ( 930) hydrogen bonds : angle 5.24417 ( 2574) covalent geometry : bond 0.00229 (25962) covalent geometry : angle 0.52019 (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 : 2.625 Fit side-chains REVERT: A 113 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 256 ASN cc_start: 0.8612 (t0) cc_final: 0.8298 (t0) REVERT: A 288 SER cc_start: 0.7893 (m) cc_final: 0.7644 (p) REVERT: A 428 LYS cc_start: 0.8507 (mttm) cc_final: 0.8193 (mmtm) REVERT: A 430 MET cc_start: 0.7351 (tpt) cc_final: 0.7133 (tpt) REVERT: F 113 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8349 (mt) REVERT: F 288 SER cc_start: 0.8183 (m) cc_final: 0.7894 (p) REVERT: F 344 GLN cc_start: 0.8136 (pt0) cc_final: 0.7876 (pt0) REVERT: B 113 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8254 (mt) REVERT: B 288 SER cc_start: 0.7901 (m) cc_final: 0.7661 (p) REVERT: B 428 LYS cc_start: 0.8504 (mttm) cc_final: 0.8190 (mmtm) REVERT: B 430 MET cc_start: 0.7377 (tpt) cc_final: 0.7153 (tpt) REVERT: C 113 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8344 (mt) REVERT: C 288 SER cc_start: 0.8160 (m) cc_final: 0.7872 (p) REVERT: C 344 GLN cc_start: 0.8141 (pt0) cc_final: 0.7882 (pt0) REVERT: D 113 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8237 (mt) REVERT: D 232 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8383 (mm) REVERT: D 288 SER cc_start: 0.7973 (m) cc_final: 0.7578 (p) REVERT: E 113 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8222 (mt) REVERT: E 232 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8381 (mm) REVERT: E 288 SER cc_start: 0.7971 (m) cc_final: 0.7587 (p) REVERT: E 428 LYS cc_start: 0.8525 (mttm) cc_final: 0.8132 (mmtt) outliers start: 38 outliers final: 4 residues processed: 311 average time/residue: 1.4604 time to fit residues: 520.8204 Evaluate side-chains 278 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 266 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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: 1.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 316 optimal weight: 0.0370 chunk 74 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 240 optimal weight: 0.5980 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.168944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100105 restraints weight = 23951.254| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.98 r_work: 0.3119 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 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 = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25962 Z= 0.118 Angle : 0.520 7.293 35196 Z= 0.275 Chirality : 0.045 0.145 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.260 84.003 3492 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.50 % Favored : 96.12 % Rotamer: Outliers : 1.30 % Allowed : 16.88 % 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: 1.25 (0.16), residues: 1086 sheet: 0.39 (0.23), residues: 510 loop : -0.70 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 402 HIS 0.003 0.001 HIS C 39 PHE 0.013 0.001 PHE B 225 TYR 0.011 0.001 TYR A 245 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 930) hydrogen bonds : angle 5.18246 ( 2574) covalent geometry : bond 0.00262 (25962) covalent geometry : angle 0.51957 (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 315 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 2.825 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: 0.8684 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 256 ASN cc_start: 0.8634 (t0) cc_final: 0.8319 (t0) REVERT: A 288 SER cc_start: 0.7888 (m) cc_final: 0.7629 (p) REVERT: A 428 LYS cc_start: 0.8512 (mttm) cc_final: 0.8195 (mmtm) REVERT: F 61 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8558 (mtmm) REVERT: F 113 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8431 (mt) REVERT: F 288 SER cc_start: 0.8010 (m) cc_final: 0.7746 (p) REVERT: B 113 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 288 SER cc_start: 0.7895 (m) cc_final: 0.7642 (p) REVERT: B 428 LYS cc_start: 0.8510 (mttm) cc_final: 0.8184 (mmtm) REVERT: C 61 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8547 (mtmm) REVERT: C 113 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8435 (mt) REVERT: C 288 SER cc_start: 0.8007 (m) cc_final: 0.7744 (p) REVERT: D 113 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8325 (mt) REVERT: D 232 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8398 (mm) REVERT: D 281 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7639 (ttpt) REVERT: D 288 SER cc_start: 0.8014 (m) cc_final: 0.7640 (p) REVERT: D 428 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8125 (mmtp) REVERT: E 113 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8321 (mt) REVERT: E 232 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8394 (mm) REVERT: E 281 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7635 (ttpt) REVERT: E 288 SER cc_start: 0.8014 (m) cc_final: 0.7643 (p) REVERT: E 428 LYS cc_start: 0.8499 (mttm) cc_final: 0.8099 (mmtt) outliers start: 36 outliers final: 14 residues processed: 311 average time/residue: 1.4913 time to fit residues: 533.6226 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 : 2.701 ------------------------------------------------------------------------------- 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: 0.8980 chunk 187 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 317 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.168322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100710 restraints weight = 23815.097| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.15 r_work: 0.3067 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 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 = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1683 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= 0.143 Angle : 0.538 7.337 35196 Z= 0.285 Chirality : 0.046 0.147 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.364 85.199 3492 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.69 % Favored : 95.93 % Rotamer: Outliers : 1.41 % Allowed : 16.52 % Favored : 82.07 % 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: 0.20 (0.15), residues: 3168 helix: 1.21 (0.16), residues: 1086 sheet: 0.34 (0.22), residues: 510 loop : -0.67 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 402 HIS 0.003 0.001 HIS C 39 PHE 0.014 0.002 PHE E 225 TYR 0.013 0.001 TYR A 245 ARG 0.002 0.000 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 930) hydrogen bonds : angle 5.25478 ( 2574) covalent geometry : bond 0.00322 (25962) covalent geometry : angle 0.53795 (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 317 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 2.623 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: 0.8813 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 256 ASN cc_start: 0.8644 (t0) cc_final: 0.8318 (t0) REVERT: A 288 SER cc_start: 0.7928 (m) cc_final: 0.7654 (p) REVERT: A 428 LYS cc_start: 0.8540 (mttm) cc_final: 0.8219 (mmtm) REVERT: F 61 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8590 (mtmm) REVERT: F 113 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8548 (mt) REVERT: F 288 SER cc_start: 0.8012 (m) cc_final: 0.7728 (p) REVERT: F 331 GLN cc_start: 0.7714 (mm110) cc_final: 0.6937 (mt0) REVERT: B 113 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 288 SER cc_start: 0.7932 (m) cc_final: 0.7660 (p) REVERT: B 428 LYS cc_start: 0.8552 (mttm) cc_final: 0.8218 (mmtm) REVERT: C 61 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8580 (mtmm) REVERT: C 113 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8552 (mt) REVERT: C 288 SER cc_start: 0.8004 (m) cc_final: 0.7720 (p) REVERT: C 331 GLN cc_start: 0.7710 (mm110) cc_final: 0.6934 (mt0) REVERT: D 113 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8527 (mt) REVERT: D 232 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8420 (mm) REVERT: D 281 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7607 (ttpt) REVERT: D 288 SER cc_start: 0.8101 (m) cc_final: 0.7715 (p) REVERT: D 428 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8097 (mmtp) REVERT: E 113 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8525 (mt) REVERT: E 232 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 281 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7611 (ttpt) REVERT: E 288 SER cc_start: 0.8100 (m) cc_final: 0.7710 (p) REVERT: E 428 LYS cc_start: 0.8521 (mttm) cc_final: 0.8088 (mmtt) outliers start: 39 outliers final: 14 residues processed: 315 average time/residue: 1.4139 time to fit residues: 512.0051 Evaluate side-chains 295 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 2.737 ------------------------------------------------------------------------------- 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 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 44 optimal weight: 50.0000 chunk 217 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 209 optimal weight: 0.0670 chunk 139 optimal weight: 4.9990 chunk 263 optimal weight: 0.0170 chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.169677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102377 restraints weight = 23743.607| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.04 r_work: 0.3121 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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 = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1786 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= 0.099 Angle : 0.498 7.067 35196 Z= 0.263 Chirality : 0.044 0.138 3978 Planarity : 0.003 0.032 4488 Dihedral : 6.198 87.877 3492 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.47 % Favored : 96.15 % Rotamer: Outliers : 1.30 % Allowed : 16.74 % 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: 0.31 (0.15), residues: 3168 helix: 1.35 (0.16), residues: 1086 sheet: 0.32 (0.22), residues: 510 loop : -0.62 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 402 HIS 0.003 0.001 HIS D 39 PHE 0.012 0.001 PHE B 225 TYR 0.009 0.001 TYR B 245 ARG 0.002 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 930) hydrogen bonds : angle 4.99026 ( 2574) covalent geometry : bond 0.00218 (25962) covalent geometry : angle 0.49834 (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 311 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 3.136 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: 0.8569 (OUTLIER) cc_final: 0.8255 (mt) REVERT: A 256 ASN cc_start: 0.8646 (t0) cc_final: 0.8315 (t0) REVERT: A 288 SER cc_start: 0.7843 (m) cc_final: 0.7573 (p) REVERT: A 428 LYS cc_start: 0.8585 (mttm) cc_final: 0.8290 (mmtm) REVERT: F 61 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8590 (mtmm) REVERT: F 113 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8336 (mt) REVERT: F 288 SER cc_start: 0.7893 (m) cc_final: 0.7638 (p) REVERT: F 331 GLN cc_start: 0.7635 (mm110) cc_final: 0.6886 (mt0) REVERT: B 113 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (mt) REVERT: B 288 SER cc_start: 0.7841 (m) cc_final: 0.7569 (p) REVERT: B 428 LYS cc_start: 0.8585 (mttm) cc_final: 0.8287 (mmtm) REVERT: C 61 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8575 (mtmm) REVERT: C 113 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8336 (mt) REVERT: C 288 SER cc_start: 0.7889 (m) cc_final: 0.7635 (p) REVERT: C 331 GLN cc_start: 0.7634 (mm110) cc_final: 0.6886 (mt0) REVERT: D 113 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8272 (mt) REVERT: D 232 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8304 (mm) REVERT: D 281 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7615 (ttpt) REVERT: D 288 SER cc_start: 0.7962 (m) cc_final: 0.7631 (p) REVERT: D 428 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8117 (mmtp) REVERT: E 113 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8270 (mt) REVERT: E 232 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8308 (mm) REVERT: E 281 LYS cc_start: 0.8419 (ttpt) cc_final: 0.7607 (ttpt) REVERT: E 288 SER cc_start: 0.7959 (m) cc_final: 0.7635 (p) REVERT: E 428 LYS cc_start: 0.8601 (mttm) cc_final: 0.8183 (mmtt) outliers start: 36 outliers final: 16 residues processed: 307 average time/residue: 1.3824 time to fit residues: 490.0917 Evaluate side-chains 295 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 2.606 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 59 optimal weight: 5.9990 chunk 188 optimal weight: 0.1980 chunk 237 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 254 optimal weight: 0.0770 chunk 114 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.169594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104265 restraints weight = 23832.886| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.15 r_work: 0.3111 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 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 = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25962 Z= 0.102 Angle : 0.499 7.206 35196 Z= 0.263 Chirality : 0.044 0.141 3978 Planarity : 0.003 0.031 4488 Dihedral : 6.208 89.977 3492 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.79 % Favored : 95.83 % Rotamer: Outliers : 1.23 % Allowed : 17.14 % 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: 0.35 (0.15), residues: 3168 helix: 1.39 (0.16), residues: 1086 sheet: 0.32 (0.22), residues: 510 loop : -0.59 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 402 HIS 0.003 0.001 HIS E 39 PHE 0.012 0.001 PHE B 225 TYR 0.010 0.001 TYR B 245 ARG 0.002 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 930) hydrogen bonds : angle 4.96201 ( 2574) covalent geometry : bond 0.00226 (25962) covalent geometry : angle 0.49918 (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 308 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 2.830 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: 0.8615 (OUTLIER) cc_final: 0.8289 (mt) REVERT: A 256 ASN cc_start: 0.8654 (t0) cc_final: 0.8319 (t0) REVERT: A 288 SER cc_start: 0.7838 (m) cc_final: 0.7582 (p) REVERT: A 428 LYS cc_start: 0.8553 (mttm) cc_final: 0.8258 (mmtm) REVERT: F 61 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8617 (mtmm) REVERT: F 113 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8327 (mt) REVERT: F 288 SER cc_start: 0.7893 (m) cc_final: 0.7629 (p) REVERT: F 331 GLN cc_start: 0.7602 (mm110) cc_final: 0.6853 (mt0) REVERT: B 113 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8282 (mt) REVERT: B 288 SER cc_start: 0.7844 (m) cc_final: 0.7563 (p) REVERT: B 428 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8257 (mmtm) REVERT: C 61 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8605 (mtmm) REVERT: C 113 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8324 (mt) REVERT: C 288 SER cc_start: 0.7885 (m) cc_final: 0.7636 (p) REVERT: C 331 GLN cc_start: 0.7596 (mm110) cc_final: 0.6848 (mt0) REVERT: D 113 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8257 (mt) REVERT: D 232 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8321 (mm) REVERT: D 281 LYS cc_start: 0.8421 (ttpt) cc_final: 0.7602 (ttpt) REVERT: D 288 SER cc_start: 0.7951 (m) cc_final: 0.7631 (p) REVERT: D 428 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8105 (mmtp) REVERT: E 113 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8251 (mt) REVERT: E 232 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8319 (mm) REVERT: E 281 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7606 (ttpt) REVERT: E 288 SER cc_start: 0.7952 (m) cc_final: 0.7640 (p) REVERT: E 428 LYS cc_start: 0.8582 (mttm) cc_final: 0.8140 (mmtt) outliers start: 34 outliers final: 16 residues processed: 305 average time/residue: 1.4248 time to fit residues: 500.6338 Evaluate side-chains 297 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 2.696 ------------------------------------------------------------------------------- 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 428 LYS 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: 1.9990 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 chunk 302 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 246 optimal weight: 0.9980 chunk 282 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.166755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.097925 restraints weight = 23682.022| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.96 r_work: 0.3084 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25962 Z= 0.180 Angle : 0.567 10.137 35196 Z= 0.299 Chirality : 0.048 0.153 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.465 87.754 3492 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.44 % Favored : 96.18 % Rotamer: Outliers : 1.19 % Allowed : 17.06 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.16), residues: 1086 sheet: 0.26 (0.22), residues: 510 loop : -0.61 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 402 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.002 PHE D 225 TYR 0.017 0.002 TYR A 245 ARG 0.004 0.001 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 930) hydrogen bonds : angle 5.32797 ( 2574) covalent geometry : bond 0.00410 (25962) covalent geometry : angle 0.56738 (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 306 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 2.810 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: 0.8924 (OUTLIER) cc_final: 0.8636 (mt) REVERT: A 256 ASN cc_start: 0.8674 (t0) cc_final: 0.8343 (t0) REVERT: A 288 SER cc_start: 0.7861 (m) cc_final: 0.7618 (p) REVERT: A 428 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8253 (mmtm) REVERT: F 61 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8647 (mtmm) REVERT: F 113 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8627 (mt) REVERT: F 288 SER cc_start: 0.8005 (m) cc_final: 0.7735 (p) REVERT: F 331 GLN cc_start: 0.7575 (mm110) cc_final: 0.6842 (mt0) REVERT: B 113 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 288 SER cc_start: 0.7863 (m) cc_final: 0.7623 (p) REVERT: B 428 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8257 (mmtm) REVERT: C 61 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8641 (mtmm) REVERT: C 113 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8633 (mt) REVERT: C 288 SER cc_start: 0.7943 (m) cc_final: 0.7671 (p) REVERT: C 331 GLN cc_start: 0.7575 (mm110) cc_final: 0.6843 (mt0) REVERT: D 113 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8652 (mt) REVERT: D 232 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8433 (mm) REVERT: D 288 SER cc_start: 0.8071 (m) cc_final: 0.7716 (p) REVERT: E 113 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8651 (mt) REVERT: E 232 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8431 (mm) REVERT: E 288 SER cc_start: 0.8071 (m) cc_final: 0.7721 (p) outliers start: 33 outliers final: 12 residues processed: 303 average time/residue: 1.4650 time to fit residues: 509.8755 Evaluate side-chains 289 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 2.961 ------------------------------------------------------------------------------- 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 428 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 143 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.168488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100029 restraints weight = 23844.562| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.97 r_work: 0.3120 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 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 = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1910 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= 0.118 Angle : 0.518 8.308 35196 Z= 0.273 Chirality : 0.045 0.141 3978 Planarity : 0.004 0.031 4488 Dihedral : 6.283 88.985 3492 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.82 % Favored : 95.80 % Rotamer: Outliers : 1.12 % Allowed : 17.21 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.22), residues: 510 loop : -0.58 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 402 HIS 0.003 0.001 HIS D 39 PHE 0.013 0.001 PHE B 225 TYR 0.011 0.001 TYR A 245 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 930) hydrogen bonds : angle 5.09513 ( 2574) covalent geometry : bond 0.00266 (25962) covalent geometry : angle 0.51774 (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 304 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 2.976 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: 0.8709 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 256 ASN cc_start: 0.8653 (t0) cc_final: 0.8307 (t0) REVERT: A 288 SER cc_start: 0.7854 (m) cc_final: 0.7596 (p) REVERT: A 428 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8247 (mmtm) REVERT: F 61 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8627 (mtmm) REVERT: F 113 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (mt) REVERT: F 288 SER cc_start: 0.7897 (m) cc_final: 0.7641 (p) REVERT: F 331 GLN cc_start: 0.7578 (mm110) cc_final: 0.6873 (mt0) REVERT: B 113 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 256 ASN cc_start: 0.8583 (t0) cc_final: 0.8219 (t0) REVERT: B 288 SER cc_start: 0.7871 (m) cc_final: 0.7609 (p) REVERT: B 428 LYS cc_start: 0.8524 (mttm) cc_final: 0.8246 (mmtm) REVERT: C 61 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8618 (mtmm) REVERT: C 113 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8447 (mt) REVERT: C 288 SER cc_start: 0.7897 (m) cc_final: 0.7644 (p) REVERT: C 331 GLN cc_start: 0.7571 (mm110) cc_final: 0.6867 (mt0) REVERT: D 113 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8429 (mt) REVERT: D 154 GLN cc_start: 0.7761 (pt0) cc_final: 0.7462 (mm110) REVERT: D 232 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8372 (mm) REVERT: D 281 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7613 (ttpt) REVERT: D 288 SER cc_start: 0.7981 (m) cc_final: 0.7663 (p) REVERT: D 428 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8088 (mmtp) REVERT: E 113 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8428 (mt) REVERT: E 154 GLN cc_start: 0.7779 (pt0) cc_final: 0.7464 (mm110) REVERT: E 232 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8365 (mm) REVERT: E 281 LYS cc_start: 0.8416 (ttpt) cc_final: 0.7605 (ttpt) REVERT: E 288 SER cc_start: 0.7982 (m) cc_final: 0.7671 (p) outliers start: 31 outliers final: 14 residues processed: 301 average time/residue: 1.4781 time to fit residues: 514.7329 Evaluate side-chains 300 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 2.847 ------------------------------------------------------------------------------- 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 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 132 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.0070 chunk 136 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 276 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.168081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099553 restraints weight = 23742.529| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.98 r_work: 0.3112 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25962 Z= 0.127 Angle : 0.529 10.173 35196 Z= 0.278 Chirality : 0.045 0.145 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.315 89.905 3492 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.38 % Favored : 96.24 % Rotamer: Outliers : 1.05 % Allowed : 17.28 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.16), residues: 1086 sheet: 0.23 (0.22), residues: 510 loop : -0.56 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 402 HIS 0.003 0.001 HIS C 39 PHE 0.014 0.001 PHE B 225 TYR 0.012 0.001 TYR B 245 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 930) hydrogen bonds : angle 5.12658 ( 2574) covalent geometry : bond 0.00286 (25962) covalent geometry : angle 0.52939 (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 306 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 2.849 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: 0.8754 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 238 MET cc_start: 0.8718 (tpt) cc_final: 0.6857 (tpt) REVERT: A 256 ASN cc_start: 0.8655 (t0) cc_final: 0.8314 (t0) REVERT: A 288 SER cc_start: 0.7873 (m) cc_final: 0.7616 (p) REVERT: A 428 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8267 (mmtm) REVERT: F 61 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8628 (mtmm) REVERT: F 113 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8483 (mt) REVERT: F 288 SER cc_start: 0.7888 (m) cc_final: 0.7621 (p) REVERT: B 113 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 238 MET cc_start: 0.8710 (tpt) cc_final: 0.6959 (tpt) REVERT: B 256 ASN cc_start: 0.8563 (t0) cc_final: 0.8201 (t0) REVERT: B 288 SER cc_start: 0.7868 (m) cc_final: 0.7611 (p) REVERT: B 428 LYS cc_start: 0.8545 (mttm) cc_final: 0.8272 (mmtm) REVERT: C 61 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8619 (mtmm) REVERT: C 113 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8485 (mt) REVERT: C 288 SER cc_start: 0.7892 (m) cc_final: 0.7628 (p) REVERT: D 113 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8463 (mt) REVERT: D 154 GLN cc_start: 0.7725 (pt0) cc_final: 0.7454 (mm110) REVERT: D 232 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8428 (mm) REVERT: D 281 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7608 (ttpt) REVERT: D 288 SER cc_start: 0.7966 (m) cc_final: 0.7648 (p) REVERT: D 428 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8154 (mmtm) REVERT: E 113 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (mt) REVERT: E 154 GLN cc_start: 0.7735 (pt0) cc_final: 0.7457 (mm110) REVERT: E 232 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8427 (mm) REVERT: E 281 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7604 (ttpt) REVERT: E 288 SER cc_start: 0.7968 (m) cc_final: 0.7661 (p) REVERT: E 428 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8199 (mmtm) outliers start: 29 outliers final: 14 residues processed: 304 average time/residue: 1.4634 time to fit residues: 510.4237 Evaluate side-chains 299 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 135 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 153 optimal weight: 0.0970 chunk 311 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 114 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.168812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103448 restraints weight = 23791.417| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.18 r_work: 0.3089 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- 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: 0.8473 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25962 Z= 0.110 Angle : 0.513 9.416 35196 Z= 0.269 Chirality : 0.045 0.141 3978 Planarity : 0.003 0.032 4488 Dihedral : 6.237 89.758 3492 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 1.05 % Allowed : 17.28 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.16), residues: 1086 sheet: 0.24 (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 B 225 TYR 0.010 0.001 TYR B 245 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 930) hydrogen bonds : angle 5.02239 ( 2574) covalent geometry : bond 0.00248 (25962) covalent geometry : angle 0.51260 (35196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26957.88 seconds wall clock time: 465 minutes 23.58 seconds (27923.58 seconds total)