Starting phenix.real_space_refine on Mon Sep 30 10:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/09_2024/8i22_35129_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/09_2024/8i22_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/09_2024/8i22_35129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/09_2024/8i22_35129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/09_2024/8i22_35129_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/09_2024/8i22_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-5461/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: 14.43, per 1000 atoms: 0.57 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: 6.35 Conformation dependent library (CDL) restraints added in 3.3 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: 3.40 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: 10.16 Time building geometry restraints manager: 7.26 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 57.660 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.360 ------------------------------------------------------------------------------- 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= 0.422 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 *********************** 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 fitting. rotamer outliers: 18 poor density : 308 time to evaluate : 2.813 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: 1.5294 time to fit residues: 566.8918 Evaluate side-chains 261 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 252 time to evaluate : 2.843 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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= 0.238 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 *********************** 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 fitting. rotamer outliers: 46 poor density : 279 time to evaluate : 3.073 Fit side-chains REVERT: A 113 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 256 ASN cc_start: 0.8522 (t0) cc_final: 0.8300 (t0) REVERT: A 430 MET cc_start: 0.7848 (tpt) cc_final: 0.7627 (tpt) REVERT: F 197 MET cc_start: 0.8564 (mmp) cc_final: 0.8111 (mtp) REVERT: F 344 GLN cc_start: 0.8356 (pt0) cc_final: 0.8148 (pt0) REVERT: B 113 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8332 (mt) REVERT: C 197 MET cc_start: 0.8566 (mmp) cc_final: 0.8112 (mtp) REVERT: C 344 GLN cc_start: 0.8356 (pt0) cc_final: 0.8146 (pt0) REVERT: D 113 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (mt) REVERT: E 113 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8372 (mt) outliers start: 46 outliers final: 2 residues processed: 323 average time/residue: 1.4502 time to fit residues: 536.5289 Evaluate side-chains 261 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 255 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 222 THR 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 160 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 0.0870 chunk 257 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 260 GLN D 395 ASN E 260 GLN E 395 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25962 Z= 0.195 Angle : 0.546 7.316 35196 Z= 0.289 Chirality : 0.046 0.144 3978 Planarity : 0.004 0.035 4488 Dihedral : 6.363 77.679 3492 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 1.37 % Allowed : 16.20 % Favored : 82.43 % 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: 0.06 (0.15), residues: 3168 helix: 1.09 (0.16), residues: 1086 sheet: 0.35 (0.23), residues: 510 loop : -0.81 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 402 HIS 0.003 0.001 HIS E 39 PHE 0.013 0.001 PHE D 225 TYR 0.012 0.001 TYR A 245 ARG 0.002 0.000 ARG A 47 *********************** 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 306 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 2.883 Fit side-chains REVERT: A 113 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 256 ASN cc_start: 0.8521 (t0) cc_final: 0.8303 (t0) REVERT: A 430 MET cc_start: 0.7806 (tpt) cc_final: 0.7580 (tpt) REVERT: A 461 MET cc_start: 0.5152 (pmm) cc_final: 0.4713 (pmt) REVERT: F 61 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8250 (mtmm) REVERT: F 197 MET cc_start: 0.8567 (mmp) cc_final: 0.8114 (mtp) REVERT: F 344 GLN cc_start: 0.8315 (pt0) cc_final: 0.8090 (pt0) REVERT: B 113 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8147 (mt) REVERT: B 430 MET cc_start: 0.7788 (tpt) cc_final: 0.7566 (tpt) REVERT: C 61 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8248 (mtmm) REVERT: C 197 MET cc_start: 0.8569 (mmp) cc_final: 0.8116 (mtp) REVERT: C 344 GLN cc_start: 0.8312 (pt0) cc_final: 0.8086 (pt0) REVERT: D 113 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8233 (mt) REVERT: D 232 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8381 (mm) REVERT: E 113 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8233 (mt) REVERT: E 232 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8377 (mm) outliers start: 38 outliers final: 4 residues processed: 302 average time/residue: 1.4772 time to fit residues: 510.4348 Evaluate side-chains 273 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 61 LYS 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 285 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 40.0000 chunk 32 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN D 154 GLN D 260 GLN E 154 GLN E 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25962 Z= 0.326 Angle : 0.603 7.726 35196 Z= 0.321 Chirality : 0.049 0.151 3978 Planarity : 0.004 0.036 4488 Dihedral : 6.582 77.348 3492 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.47 % Favored : 96.15 % Rotamer: Outliers : 1.45 % Allowed : 15.73 % Favored : 82.83 % 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: 0.05 (0.15), residues: 3168 helix: 1.03 (0.16), residues: 1080 sheet: 0.31 (0.22), residues: 510 loop : -0.74 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 402 HIS 0.005 0.001 HIS C 213 PHE 0.017 0.002 PHE E 225 TYR 0.018 0.002 TYR A 245 ARG 0.003 0.001 ARG F 190 *********************** 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 307 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 MET cc_start: 0.5325 (pmm) cc_final: 0.4940 (pmt) REVERT: F 197 MET cc_start: 0.8738 (mmp) cc_final: 0.8195 (mtp) REVERT: F 232 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8767 (mm) REVERT: C 61 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8294 (mtmm) REVERT: C 197 MET cc_start: 0.8740 (mmp) cc_final: 0.8196 (mtp) REVERT: C 232 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8763 (mm) REVERT: D 281 LYS cc_start: 0.8566 (ttpt) cc_final: 0.7860 (ttpt) REVERT: E 281 LYS cc_start: 0.8564 (ttpt) cc_final: 0.7859 (ttpt) outliers start: 40 outliers final: 13 residues processed: 303 average time/residue: 1.4668 time to fit residues: 508.6816 Evaluate side-chains 277 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 221 ILE 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 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 463 HIS 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 255 optimal weight: 0.3980 chunk 174 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 262 optimal weight: 0.0770 chunk 212 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 331 GLN F 344 GLN C 344 GLN D 154 GLN D 344 GLN E 154 GLN E 344 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1741 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= 0.144 Angle : 0.507 7.133 35196 Z= 0.269 Chirality : 0.044 0.135 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.181 80.647 3492 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.79 % Favored : 95.83 % Rotamer: Outliers : 1.19 % Allowed : 16.52 % Favored : 82.28 % 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: 1.24 (0.16), residues: 1086 sheet: 0.26 (0.22), residues: 510 loop : -0.67 (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 D 39 PHE 0.012 0.001 PHE B 225 TYR 0.010 0.001 TYR A 245 ARG 0.002 0.000 ARG E 47 *********************** 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 300 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8536 (t0) cc_final: 0.8322 (t0) REVERT: F 331 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7083 (mt0) REVERT: C 331 GLN cc_start: 0.7653 (mm110) cc_final: 0.7091 (mt0) REVERT: D 113 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8226 (mt) REVERT: D 281 LYS cc_start: 0.8502 (ttpt) cc_final: 0.7845 (ttpt) REVERT: E 113 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8221 (mt) REVERT: E 281 LYS cc_start: 0.8500 (ttpt) cc_final: 0.7844 (ttpt) outliers start: 33 outliers final: 12 residues processed: 297 average time/residue: 1.4646 time to fit residues: 500.0293 Evaluate side-chains 270 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 256 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 463 HIS 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 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP 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 463 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 307 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1792 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= 0.202 Angle : 0.532 7.417 35196 Z= 0.282 Chirality : 0.046 0.144 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.255 81.147 3492 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.57 % Favored : 96.05 % Rotamer: Outliers : 1.16 % Allowed : 16.63 % Favored : 82.21 % 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: 0.26 (0.22), residues: 510 loop : -0.65 (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 E 39 PHE 0.014 0.001 PHE B 225 TYR 0.014 0.001 TYR A 245 ARG 0.002 0.000 ARG D 47 *********************** 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 296 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 264 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8546 (t0) cc_final: 0.8322 (t0) REVERT: A 461 MET cc_start: 0.5118 (pmm) cc_final: 0.4821 (pmt) REVERT: F 331 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7115 (mt0) REVERT: B 461 MET cc_start: 0.5120 (pmm) cc_final: 0.4826 (pmt) REVERT: C 331 GLN cc_start: 0.7648 (mm110) cc_final: 0.7146 (mt0) REVERT: D 113 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8319 (mt) REVERT: D 232 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8344 (mm) REVERT: D 281 LYS cc_start: 0.8525 (ttpt) cc_final: 0.7868 (ttpt) REVERT: D 428 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8334 (mmtt) REVERT: E 113 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8320 (mt) REVERT: E 232 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8341 (mm) REVERT: E 281 LYS cc_start: 0.8522 (ttpt) cc_final: 0.7866 (ttpt) REVERT: E 428 LYS cc_start: 0.8566 (mmtp) cc_final: 0.8343 (mmtm) outliers start: 32 outliers final: 16 residues processed: 294 average time/residue: 1.4815 time to fit residues: 499.2757 Evaluate side-chains 279 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 224 optimal weight: 0.5980 chunk 174 optimal weight: 0.0040 chunk 259 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 D 331 GLN E 154 GLN E 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1836 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= 0.155 Angle : 0.506 7.118 35196 Z= 0.268 Chirality : 0.045 0.139 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.146 82.598 3492 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 0.94 % Allowed : 16.74 % Favored : 82.32 % 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: 1.29 (0.16), residues: 1086 sheet: 0.25 (0.22), residues: 510 loop : -0.61 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 402 HIS 0.003 0.001 HIS E 39 PHE 0.012 0.001 PHE E 225 TYR 0.011 0.001 TYR A 245 ARG 0.002 0.000 ARG A 47 *********************** 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 289 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8186 (mpm) REVERT: A 256 ASN cc_start: 0.8533 (t0) cc_final: 0.8313 (t0) REVERT: F 331 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7100 (mt0) REVERT: B 197 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8184 (mpm) REVERT: C 331 GLN cc_start: 0.7567 (mm110) cc_final: 0.7093 (mt0) REVERT: D 113 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8126 (mt) REVERT: D 232 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8277 (mm) REVERT: D 281 LYS cc_start: 0.8499 (ttpt) cc_final: 0.7841 (ttpt) REVERT: D 428 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8345 (mmtm) REVERT: E 113 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (mt) REVERT: E 232 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8272 (mm) REVERT: E 281 LYS cc_start: 0.8497 (ttpt) cc_final: 0.7839 (ttpt) outliers start: 26 outliers final: 14 residues processed: 287 average time/residue: 1.4390 time to fit residues: 475.5227 Evaluate side-chains 278 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 463 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 151 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN F 344 GLN D 344 GLN E 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1887 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= 0.267 Angle : 0.566 9.452 35196 Z= 0.299 Chirality : 0.047 0.151 3978 Planarity : 0.004 0.033 4488 Dihedral : 6.358 81.003 3492 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.50 % Favored : 96.12 % Rotamer: Outliers : 0.87 % Allowed : 17.06 % 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: 0.17 (0.15), residues: 3168 helix: 1.13 (0.16), residues: 1086 sheet: 0.23 (0.22), residues: 510 loop : -0.60 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 402 HIS 0.004 0.001 HIS E 74 PHE 0.015 0.002 PHE E 225 TYR 0.017 0.002 TYR A 245 ARG 0.003 0.001 ARG F 211 *********************** 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 284 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8573 (t0) cc_final: 0.8333 (t0) REVERT: F 331 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7106 (mt0) REVERT: C 331 GLN cc_start: 0.7587 (mm110) cc_final: 0.7124 (mt0) REVERT: D 113 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8464 (mt) REVERT: D 232 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8402 (mm) REVERT: E 113 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8465 (mt) REVERT: E 232 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8397 (mm) outliers start: 24 outliers final: 14 residues processed: 282 average time/residue: 1.4355 time to fit residues: 465.4528 Evaluate side-chains 272 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 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 278 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 284 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN F 214 GLN B 331 GLN C 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25962 Z= 0.292 Angle : 0.588 10.872 35196 Z= 0.312 Chirality : 0.048 0.149 3978 Planarity : 0.004 0.034 4488 Dihedral : 6.406 77.545 3492 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.60 % Favored : 96.02 % Rotamer: Outliers : 0.90 % Allowed : 16.99 % 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: 0.14 (0.15), residues: 3168 helix: 1.09 (0.16), residues: 1080 sheet: 0.18 (0.22), residues: 510 loop : -0.59 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 402 HIS 0.004 0.001 HIS D 267 PHE 0.016 0.002 PHE E 225 TYR 0.017 0.002 TYR A 245 ARG 0.003 0.001 ARG D 211 *********************** 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 281 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8561 (tpt) cc_final: 0.7031 (tpt) REVERT: F 331 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7193 (mt0) REVERT: B 238 MET cc_start: 0.8562 (tpt) cc_final: 0.7027 (tpt) REVERT: C 331 GLN cc_start: 0.7606 (mm110) cc_final: 0.7172 (mt0) REVERT: D 232 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8380 (mm) REVERT: D 281 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7881 (ttpt) REVERT: E 232 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8409 (mm) REVERT: E 281 LYS cc_start: 0.8512 (ttpt) cc_final: 0.7880 (ttpt) outliers start: 25 outliers final: 12 residues processed: 279 average time/residue: 1.4512 time to fit residues: 465.9906 Evaluate side-chains 266 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 463 HIS 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 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 187 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 0.0040 chunk 316 optimal weight: 0.0020 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- 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 344 GLN E 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2067 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= 0.140 Angle : 0.500 7.025 35196 Z= 0.264 Chirality : 0.044 0.135 3978 Planarity : 0.003 0.031 4488 Dihedral : 5.983 80.163 3492 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.28 % Favored : 96.34 % Rotamer: Outliers : 0.65 % Allowed : 17.61 % 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: 0.29 (0.15), residues: 3168 helix: 1.28 (0.16), residues: 1086 sheet: 0.17 (0.22), residues: 510 loop : -0.54 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS D 39 PHE 0.012 0.001 PHE D 225 TYR 0.010 0.001 TYR D 245 ARG 0.002 0.000 ARG E 47 ********************** 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 287 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 269 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8533 (t0) cc_final: 0.8309 (t0) REVERT: F 331 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7071 (mt0) REVERT: C 331 GLN cc_start: 0.7527 (mm110) cc_final: 0.7133 (mt0) REVERT: D 113 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8158 (mt) REVERT: D 281 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7804 (ttpt) REVERT: E 113 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (mt) REVERT: E 281 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7804 (ttpt) outliers start: 18 outliers final: 8 residues processed: 283 average time/residue: 1.4026 time to fit residues: 457.7443 Evaluate side-chains 272 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain F residue 463 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain E residue 113 ILE 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 200 optimal weight: 0.0040 chunk 268 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 252 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 259 optimal weight: 0.0570 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.0912 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.167516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099164 restraints weight = 23680.907| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.97 r_work: 0.3105 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25962 Z= 0.199 Angle : 0.537 11.009 35196 Z= 0.282 Chirality : 0.046 0.145 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.131 80.783 3492 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.47 % Favored : 96.15 % Rotamer: Outliers : 0.65 % Allowed : 17.43 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3168 helix: 1.22 (0.16), residues: 1086 sheet: 0.17 (0.22), residues: 510 loop : -0.53 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 402 HIS 0.003 0.001 HIS D 39 PHE 0.014 0.001 PHE B 225 TYR 0.013 0.001 TYR A 245 ARG 0.003 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9442.68 seconds wall clock time: 167 minutes 1.21 seconds (10021.21 seconds total)