Starting phenix.real_space_refine on Fri Aug 9 06:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzx_35091/08_2024/8hzx_35091.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzx_35091/08_2024/8hzx_35091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzx_35091/08_2024/8hzx_35091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzx_35091/08_2024/8hzx_35091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzx_35091/08_2024/8hzx_35091.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzx_35091/08_2024/8hzx_35091.cif" } resolution = 2.68 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= 0.170 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 16242 2.51 5 N 4236 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25320 Number of models: 1 Model: "" Number of chains: 6 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: "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: "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 Time building chain proxies: 13.29, per 1000 atoms: 0.52 Number of scatterers: 25320 At special positions: 0 Unit cell: (169.338, 158.184, 94.302, 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 4734 8.00 N 4236 7.00 C 16242 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 - 3.50 Amino acid : False - 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: 8.92 Conformation dependent library (CDL) restraints added in 4.5 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: 114 helices and 30 sheets defined 36.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... 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: 3.661A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.749A 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 126 removed outlier: 3.589A pdb=" N LEU F 124 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.580A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.816A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET F 285 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.640A 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 439 through 449 removed outlier: 4.126A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 493 Processing helix chain 'F' and resid 524 through 532 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: 3.661A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.750A 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 126 removed outlier: 3.589A pdb=" N LEU A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.817A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.733A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.640A 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 439 through 449 removed outlier: 4.126A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 524 through 532 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: 3.661A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.749A 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 126 removed outlier: 3.589A pdb=" N LEU B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.816A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.733A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.898A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.641A 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 439 through 449 removed outlier: 4.127A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 524 through 532 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: 3.661A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.749A 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 126 removed outlier: 3.589A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.817A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.640A 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 439 through 449 removed outlier: 4.126A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 524 through 532 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: 3.661A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.750A 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 126 removed outlier: 3.589A pdb=" N LEU D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.817A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 285 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.641A 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 439 through 449 removed outlier: 4.127A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 524 through 532 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: 3.661A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.749A 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 126 removed outlier: 3.589A pdb=" N LEU E 124 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.815A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.900A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET E 285 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.640A 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 439 through 449 removed outlier: 4.126A pdb=" N LEU E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 524 through 532 Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN F 243 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER F 266 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 353 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR F 65 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU F 115 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA F 67 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS F 117 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET F 69 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE F 431 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 438 " --> pdb=" O ILE F 431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY F 467 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN A 243 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 266 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 353 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.704A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.391A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE A 431 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 438 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 467 " --> pdb=" O PRO A 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN B 243 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 266 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 353 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE B 431 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 438 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 467 " --> pdb=" O PRO B 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.196A 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: 3.542A pdb=" N GLN C 243 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 266 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 353 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE C 431 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 438 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 467 " --> pdb=" O PRO C 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.195A 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: 3.541A pdb=" N GLN D 243 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 266 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 353 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.389A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.817A pdb=" N ILE D 431 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 438 " --> pdb=" O ILE D 431 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY D 467 " --> pdb=" O PRO D 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.195A 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: 3.541A pdb=" N GLN E 243 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER E 266 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E 353 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR E 65 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU E 115 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA E 67 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS E 117 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET E 69 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE E 431 " --> pdb=" O VAL E 438 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL E 438 " --> pdb=" O ILE E 431 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY E 467 " --> pdb=" O PRO E 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.09 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4278 1.30 - 1.42: 6444 1.42 - 1.55: 14973 1.55 - 1.68: 3 1.68 - 1.80: 192 Bond restraints: 25890 Sorted by residual: bond pdb=" CA TYR E 174 " pdb=" C TYR E 174 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.22e-02 6.72e+03 3.55e+01 bond pdb=" CA TYR C 174 " pdb=" C TYR C 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.47e+01 bond pdb=" CA TYR A 174 " pdb=" C TYR A 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.47e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.46e+01 bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.44e+01 ... (remaining 25885 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.81: 507 105.81 - 112.86: 14124 112.86 - 119.90: 8707 119.90 - 126.95: 11432 126.95 - 134.00: 348 Bond angle restraints: 35118 Sorted by residual: angle pdb=" N VAL D 253 " pdb=" CA VAL D 253 " pdb=" C VAL D 253 " ideal model delta sigma weight residual 111.90 100.37 11.53 8.10e-01 1.52e+00 2.03e+02 angle pdb=" N VAL E 253 " pdb=" CA VAL E 253 " pdb=" C VAL E 253 " ideal model delta sigma weight residual 111.90 100.38 11.52 8.10e-01 1.52e+00 2.02e+02 angle pdb=" N VAL C 253 " pdb=" CA VAL C 253 " pdb=" C VAL C 253 " ideal model delta sigma weight residual 111.90 100.38 11.52 8.10e-01 1.52e+00 2.02e+02 angle pdb=" N VAL F 253 " pdb=" CA VAL F 253 " pdb=" C VAL F 253 " ideal model delta sigma weight residual 111.90 100.39 11.51 8.10e-01 1.52e+00 2.02e+02 angle pdb=" N VAL B 253 " pdb=" CA VAL B 253 " pdb=" C VAL B 253 " ideal model delta sigma weight residual 111.90 100.43 11.47 8.10e-01 1.52e+00 2.01e+02 ... (remaining 35113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 13728 17.59 - 35.18: 1332 35.18 - 52.77: 378 52.77 - 70.36: 48 70.36 - 87.95: 36 Dihedral angle restraints: 15522 sinusoidal: 6252 harmonic: 9270 Sorted by residual: dihedral pdb=" CA ALA C 504 " pdb=" C ALA C 504 " pdb=" N LEU C 505 " pdb=" CA LEU C 505 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ALA E 504 " pdb=" C ALA E 504 " pdb=" N LEU E 505 " pdb=" CA LEU E 505 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ALA F 504 " pdb=" C ALA F 504 " pdb=" N LEU F 505 " pdb=" CA LEU F 505 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3295 0.071 - 0.142: 579 0.142 - 0.214: 74 0.214 - 0.285: 24 0.285 - 0.356: 6 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CB VAL C 363 " pdb=" CA VAL C 363 " pdb=" CG1 VAL C 363 " pdb=" CG2 VAL C 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL D 363 " pdb=" CA VAL D 363 " pdb=" CG1 VAL D 363 " pdb=" CG2 VAL D 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB VAL A 363 " pdb=" CA VAL A 363 " pdb=" CG1 VAL A 363 " pdb=" CG2 VAL A 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 3975 not shown) Planarity restraints: 4476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 362 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ILE B 362 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE B 362 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 363 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 362 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C ILE D 362 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 362 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL D 363 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 362 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C ILE A 362 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE A 362 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 363 " 0.016 2.00e-02 2.50e+03 ... (remaining 4473 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 408 2.67 - 3.22: 23275 3.22 - 3.78: 38556 3.78 - 4.34: 56368 4.34 - 4.90: 91572 Nonbonded interactions: 210179 Sorted by model distance: nonbonded pdb=" OD2 ASP D 72 " pdb=" OH TYR D 249 " model vdw 2.107 3.040 nonbonded pdb=" OD2 ASP C 72 " pdb=" OH TYR C 249 " model vdw 2.108 3.040 nonbonded pdb=" OD2 ASP A 72 " pdb=" OH TYR A 249 " model vdw 2.108 3.040 nonbonded pdb=" OD2 ASP F 72 " pdb=" OH TYR F 249 " model vdw 2.108 3.040 nonbonded pdb=" OD2 ASP E 72 " pdb=" OH TYR E 249 " model vdw 2.108 3.040 ... (remaining 210174 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 63.970 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.006 0.073 25890 Z= 0.433 Angle : 0.768 11.532 35118 Z= 0.492 Chirality : 0.058 0.356 3978 Planarity : 0.005 0.029 4476 Dihedral : 15.723 87.951 9558 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % 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: -1.13 (0.14), residues: 3168 helix: 0.05 (0.16), residues: 1086 sheet: -0.84 (0.21), residues: 582 loop : -1.24 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 230 HIS 0.007 0.001 HIS D 228 PHE 0.010 0.002 PHE E 315 TYR 0.016 0.002 TYR D 174 ARG 0.006 0.001 ARG B 150 *********************** 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 210 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.770 Fit side-chains REVERT: F 150 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7619 (mtm-85) REVERT: F 154 GLN cc_start: 0.8082 (mm110) cc_final: 0.7654 (mt0) REVERT: F 163 ASP cc_start: 0.8310 (t70) cc_final: 0.8042 (t70) REVERT: F 281 LYS cc_start: 0.7465 (tttm) cc_final: 0.7163 (ptmt) REVERT: F 320 MET cc_start: 0.7417 (ppp) cc_final: 0.6900 (ppp) REVERT: F 399 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8310 (mttp) REVERT: A 154 GLN cc_start: 0.7974 (mm110) cc_final: 0.7676 (mt0) REVERT: A 320 MET cc_start: 0.7346 (ppp) cc_final: 0.6998 (ppp) REVERT: B 154 GLN cc_start: 0.8133 (mm110) cc_final: 0.7670 (mt0) REVERT: C 150 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7525 (mtm-85) REVERT: C 154 GLN cc_start: 0.8037 (mm110) cc_final: 0.7711 (mt0) REVERT: C 163 ASP cc_start: 0.8252 (t70) cc_final: 0.7960 (t70) REVERT: C 281 LYS cc_start: 0.7655 (tttm) cc_final: 0.7276 (ptmt) REVERT: C 428 LYS cc_start: 0.8611 (mttm) cc_final: 0.8369 (mptt) REVERT: D 85 MET cc_start: 0.8961 (mtt) cc_final: 0.8471 (mtt) REVERT: D 154 GLN cc_start: 0.8093 (mm110) cc_final: 0.7741 (mt0) REVERT: D 197 MET cc_start: 0.8688 (mmp) cc_final: 0.8364 (mmm) REVERT: E 85 MET cc_start: 0.8946 (mtt) cc_final: 0.8552 (mtt) REVERT: E 154 GLN cc_start: 0.8182 (mm110) cc_final: 0.7854 (mt0) REVERT: E 197 MET cc_start: 0.8603 (mmp) cc_final: 0.8303 (mmm) REVERT: E 320 MET cc_start: 0.7220 (ppp) cc_final: 0.6721 (ppp) REVERT: E 416 ASP cc_start: 0.7734 (t0) cc_final: 0.7530 (t0) REVERT: E 428 LYS cc_start: 0.8498 (mttm) cc_final: 0.8246 (mmtt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 1.6049 time to fit residues: 382.7697 Evaluate side-chains 166 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 HIS F 160 ASN F 243 GLN A 160 ASN A 243 GLN B 39 HIS B 160 ASN B 243 GLN C 108 HIS C 160 ASN C 243 GLN D 39 HIS D 108 HIS D 160 ASN D 243 GLN E 39 HIS E 108 HIS E 160 ASN E 243 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25890 Z= 0.264 Angle : 0.592 6.396 35118 Z= 0.318 Chirality : 0.047 0.180 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.261 27.301 3426 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 3.43 % Allowed : 12.73 % Favored : 83.84 % 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: -0.83 (0.15), residues: 3168 helix: 0.45 (0.16), residues: 1086 sheet: -0.70 (0.20), residues: 600 loop : -1.19 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 230 HIS 0.007 0.001 HIS B 228 PHE 0.012 0.001 PHE E 225 TYR 0.010 0.002 TYR A 174 ARG 0.004 0.001 ARG B 150 *********************** 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 269 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 174 time to evaluate : 3.143 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8546 (mtm) cc_final: 0.8319 (mtm) REVERT: F 150 ARG cc_start: 0.7922 (mmt90) cc_final: 0.7638 (mtm-85) REVERT: F 154 GLN cc_start: 0.7836 (mm110) cc_final: 0.7471 (mt0) REVERT: F 163 ASP cc_start: 0.8363 (t70) cc_final: 0.8071 (t70) REVERT: F 281 LYS cc_start: 0.7440 (tttm) cc_final: 0.7165 (ptmt) REVERT: F 320 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6873 (ppp) REVERT: A 154 GLN cc_start: 0.7797 (mm110) cc_final: 0.7410 (mt0) REVERT: B 154 GLN cc_start: 0.7902 (mm110) cc_final: 0.7507 (mt0) REVERT: B 373 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7605 (p0) REVERT: C 58 MET cc_start: 0.8342 (mtm) cc_final: 0.8048 (mtt) REVERT: C 154 GLN cc_start: 0.7783 (mm110) cc_final: 0.7479 (mt0) REVERT: C 163 ASP cc_start: 0.8318 (t70) cc_final: 0.8019 (t70) REVERT: C 281 LYS cc_start: 0.7636 (tttm) cc_final: 0.7267 (ptmt) REVERT: C 347 TYR cc_start: 0.8530 (m-80) cc_final: 0.8312 (m-80) REVERT: C 428 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8386 (mptt) REVERT: D 85 MET cc_start: 0.8982 (mtt) cc_final: 0.8546 (mtt) REVERT: D 154 GLN cc_start: 0.7963 (mm110) cc_final: 0.7614 (mt0) REVERT: D 197 MET cc_start: 0.8689 (mmp) cc_final: 0.8446 (mmm) REVERT: D 373 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7351 (p0) REVERT: E 85 MET cc_start: 0.8953 (mtt) cc_final: 0.8538 (mtt) REVERT: E 154 GLN cc_start: 0.7991 (mm110) cc_final: 0.7655 (mt0) REVERT: E 197 MET cc_start: 0.8641 (mmp) cc_final: 0.8418 (mmm) REVERT: E 320 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: E 373 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7524 (p0) REVERT: E 416 ASP cc_start: 0.7662 (t0) cc_final: 0.7447 (t0) REVERT: E 428 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8309 (mmtt) outliers start: 95 outliers final: 31 residues processed: 253 average time/residue: 1.3718 time to fit residues: 402.3900 Evaluate side-chains 197 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 312 optimal weight: 30.0000 chunk 257 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 chunk 232 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 HIS B 108 HIS C 39 HIS C 189 HIS D 189 HIS E 189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25890 Z= 0.392 Angle : 0.667 6.982 35118 Z= 0.357 Chirality : 0.051 0.210 3978 Planarity : 0.005 0.035 4476 Dihedral : 5.494 25.472 3426 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 3.15 % Allowed : 13.59 % Favored : 83.26 % 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: -0.84 (0.15), residues: 3168 helix: 0.44 (0.16), residues: 1086 sheet: -0.69 (0.19), residues: 654 loop : -1.22 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 386 HIS 0.008 0.002 HIS A 228 PHE 0.013 0.002 PHE D 225 TYR 0.012 0.002 TYR C 218 ARG 0.004 0.001 ARG E 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 248 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 161 time to evaluate : 2.762 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8593 (mtm) cc_final: 0.8337 (mtm) REVERT: F 154 GLN cc_start: 0.7951 (mm110) cc_final: 0.7591 (mt0) REVERT: F 163 ASP cc_start: 0.8415 (t70) cc_final: 0.8187 (t70) REVERT: F 281 LYS cc_start: 0.7603 (tttm) cc_final: 0.7262 (ptmt) REVERT: F 428 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8080 (mttm) REVERT: A 154 GLN cc_start: 0.7864 (mm110) cc_final: 0.7517 (mt0) REVERT: B 154 GLN cc_start: 0.7909 (mm110) cc_final: 0.7545 (mt0) REVERT: B 260 GLN cc_start: 0.8001 (tt0) cc_final: 0.7719 (tt0) REVERT: B 425 ASP cc_start: 0.7821 (t0) cc_final: 0.7503 (t70) REVERT: C 58 MET cc_start: 0.8467 (mtm) cc_final: 0.8134 (mtt) REVERT: C 154 GLN cc_start: 0.7906 (mm110) cc_final: 0.7571 (mt0) REVERT: C 163 ASP cc_start: 0.8382 (t70) cc_final: 0.8114 (t70) REVERT: D 85 MET cc_start: 0.8948 (mtt) cc_final: 0.8610 (mtt) REVERT: D 154 GLN cc_start: 0.7933 (mm110) cc_final: 0.7651 (mt0) REVERT: D 322 GLU cc_start: 0.8589 (mp0) cc_final: 0.8012 (mp0) REVERT: D 373 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7402 (p0) REVERT: E 85 MET cc_start: 0.8939 (mtt) cc_final: 0.8592 (mtt) REVERT: E 154 GLN cc_start: 0.8010 (mm110) cc_final: 0.7650 (mt0) REVERT: E 373 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7483 (p0) REVERT: E 416 ASP cc_start: 0.7666 (t0) cc_final: 0.7403 (t0) REVERT: E 428 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8357 (mmtm) outliers start: 87 outliers final: 48 residues processed: 230 average time/residue: 1.2750 time to fit residues: 343.4973 Evaluate side-chains 207 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 155 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.1980 chunk 217 optimal weight: 0.6980 chunk 150 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 0.0980 chunk 290 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25890 Z= 0.150 Angle : 0.528 9.783 35118 Z= 0.276 Chirality : 0.045 0.158 3978 Planarity : 0.004 0.030 4476 Dihedral : 4.984 28.404 3426 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.81 % Favored : 94.00 % Rotamer: Outliers : 2.53 % Allowed : 15.73 % 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: -0.45 (0.15), residues: 3168 helix: 0.98 (0.16), residues: 1086 sheet: -0.66 (0.19), residues: 648 loop : -1.07 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 290 HIS 0.006 0.001 HIS A 228 PHE 0.007 0.001 PHE C 225 TYR 0.008 0.001 TYR E 148 ARG 0.004 0.000 ARG D 130 *********************** 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 237 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 167 time to evaluate : 2.801 Fit side-chains REVERT: F 28 GLU cc_start: 0.7867 (mp0) cc_final: 0.7653 (mp0) REVERT: F 58 MET cc_start: 0.8504 (mtm) cc_final: 0.8291 (mtm) REVERT: F 154 GLN cc_start: 0.7736 (mm110) cc_final: 0.7390 (mt0) REVERT: F 163 ASP cc_start: 0.8414 (t70) cc_final: 0.8175 (t70) REVERT: F 281 LYS cc_start: 0.7478 (tttm) cc_final: 0.7157 (ptmt) REVERT: F 320 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6862 (ppp) REVERT: A 154 GLN cc_start: 0.7698 (mm110) cc_final: 0.7390 (mt0) REVERT: A 260 GLN cc_start: 0.7997 (tt0) cc_final: 0.7722 (tt0) REVERT: A 320 MET cc_start: 0.7060 (ppp) cc_final: 0.6842 (pmm) REVERT: A 337 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8363 (mm) REVERT: B 154 GLN cc_start: 0.7742 (mm110) cc_final: 0.7416 (mt0) REVERT: B 260 GLN cc_start: 0.7927 (tt0) cc_final: 0.7652 (tt0) REVERT: B 337 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 425 ASP cc_start: 0.7582 (t0) cc_final: 0.7368 (t70) REVERT: C 58 MET cc_start: 0.8318 (mtm) cc_final: 0.8055 (mtt) REVERT: C 154 GLN cc_start: 0.7692 (mm110) cc_final: 0.7373 (mt0) REVERT: C 163 ASP cc_start: 0.8391 (t70) cc_final: 0.8122 (t70) REVERT: C 281 LYS cc_start: 0.7454 (tttm) cc_final: 0.7204 (ptmt) REVERT: C 322 GLU cc_start: 0.8303 (mp0) cc_final: 0.8083 (mp0) REVERT: D 150 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7475 (mpt-90) REVERT: D 154 GLN cc_start: 0.7756 (mm110) cc_final: 0.7556 (mt0) REVERT: E 150 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6993 (mpt-90) REVERT: E 154 GLN cc_start: 0.7810 (mm110) cc_final: 0.7523 (mt0) REVERT: E 416 ASP cc_start: 0.7512 (t0) cc_final: 0.7266 (t0) outliers start: 70 outliers final: 34 residues processed: 220 average time/residue: 1.2614 time to fit residues: 324.7556 Evaluate side-chains 200 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 0.0870 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 212 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25890 Z= 0.204 Angle : 0.555 9.521 35118 Z= 0.290 Chirality : 0.046 0.173 3978 Planarity : 0.004 0.032 4476 Dihedral : 4.993 28.436 3426 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % Rotamer: Outliers : 2.49 % Allowed : 16.02 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3168 helix: 1.05 (0.16), residues: 1086 sheet: -0.52 (0.19), residues: 666 loop : -1.10 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 230 HIS 0.006 0.001 HIS A 228 PHE 0.010 0.001 PHE E 225 TYR 0.010 0.001 TYR E 318 ARG 0.002 0.000 ARG C 150 *********************** 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 236 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 167 time to evaluate : 2.896 Fit side-chains REVERT: F 154 GLN cc_start: 0.7738 (mm110) cc_final: 0.7413 (mt0) REVERT: F 163 ASP cc_start: 0.8418 (t70) cc_final: 0.8167 (t70) REVERT: F 281 LYS cc_start: 0.7526 (tttm) cc_final: 0.7191 (ptmt) REVERT: F 320 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6874 (ppp) REVERT: F 416 ASP cc_start: 0.7474 (t70) cc_final: 0.7244 (t70) REVERT: A 154 GLN cc_start: 0.7644 (mm110) cc_final: 0.7364 (mt0) REVERT: A 260 GLN cc_start: 0.8006 (tt0) cc_final: 0.7738 (tt0) REVERT: A 337 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 154 GLN cc_start: 0.7701 (mm110) cc_final: 0.7462 (mt0) REVERT: B 260 GLN cc_start: 0.7936 (tt0) cc_final: 0.7673 (tt0) REVERT: B 337 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8420 (mm) REVERT: B 373 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7538 (p0) REVERT: B 425 ASP cc_start: 0.7593 (t0) cc_final: 0.7378 (t0) REVERT: C 154 GLN cc_start: 0.7707 (mm110) cc_final: 0.7405 (mt0) REVERT: C 163 ASP cc_start: 0.8391 (t70) cc_final: 0.8133 (t70) REVERT: C 281 LYS cc_start: 0.7485 (tttm) cc_final: 0.7226 (ptmt) REVERT: D 150 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7481 (mpt-90) REVERT: D 154 GLN cc_start: 0.7778 (mm110) cc_final: 0.7570 (mt0) REVERT: D 373 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7307 (p0) REVERT: E 150 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6984 (mpt-90) REVERT: E 154 GLN cc_start: 0.7804 (mm110) cc_final: 0.7522 (mt0) REVERT: E 373 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7465 (p0) REVERT: E 416 ASP cc_start: 0.7518 (t0) cc_final: 0.7286 (t0) outliers start: 69 outliers final: 44 residues processed: 222 average time/residue: 1.3282 time to fit residues: 344.2417 Evaluate side-chains 211 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 255 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.0270 chunk 161 optimal weight: 0.0870 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25890 Z= 0.135 Angle : 0.510 11.461 35118 Z= 0.262 Chirality : 0.044 0.143 3978 Planarity : 0.003 0.029 4476 Dihedral : 4.741 29.563 3426 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.44 % Rotamer: Outliers : 2.46 % Allowed : 17.06 % Favored : 80.48 % 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: 1.25 (0.17), residues: 1086 sheet: -0.46 (0.20), residues: 642 loop : -0.97 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS F 228 PHE 0.007 0.001 PHE F 315 TYR 0.011 0.001 TYR E 318 ARG 0.003 0.000 ARG D 130 *********************** 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 239 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 171 time to evaluate : 2.816 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8353 (mtm) cc_final: 0.8123 (ttm) REVERT: F 150 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6520 (mpt-90) REVERT: F 154 GLN cc_start: 0.7683 (mm110) cc_final: 0.7370 (mt0) REVERT: F 163 ASP cc_start: 0.8422 (t70) cc_final: 0.8173 (t70) REVERT: F 281 LYS cc_start: 0.7563 (tttm) cc_final: 0.7212 (ptmt) REVERT: F 320 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6265 (ppp) REVERT: F 322 GLU cc_start: 0.8216 (mp0) cc_final: 0.7960 (mp0) REVERT: F 416 ASP cc_start: 0.7441 (t70) cc_final: 0.7216 (t70) REVERT: A 154 GLN cc_start: 0.7572 (mm110) cc_final: 0.7324 (mt0) REVERT: A 260 GLN cc_start: 0.7990 (tt0) cc_final: 0.7740 (tt0) REVERT: A 337 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8364 (mm) REVERT: B 154 GLN cc_start: 0.7615 (mm110) cc_final: 0.7397 (mt0) REVERT: B 260 GLN cc_start: 0.7906 (tt0) cc_final: 0.7632 (tt0) REVERT: B 337 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8380 (mm) REVERT: C 154 GLN cc_start: 0.7619 (mm110) cc_final: 0.7351 (mt0) REVERT: C 281 LYS cc_start: 0.7426 (tttm) cc_final: 0.7143 (ptmt) REVERT: C 335 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: C 362 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7967 (pt) REVERT: E 150 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7154 (mpt-90) REVERT: E 154 GLN cc_start: 0.7716 (mm110) cc_final: 0.7502 (mt0) REVERT: E 373 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7439 (p0) REVERT: E 416 ASP cc_start: 0.7462 (t0) cc_final: 0.7056 (t0) REVERT: E 428 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8250 (mmtt) outliers start: 68 outliers final: 36 residues processed: 227 average time/residue: 1.3715 time to fit residues: 361.5049 Evaluate side-chains 207 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 259 optimal weight: 0.4980 chunk 171 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25890 Z= 0.221 Angle : 0.561 9.435 35118 Z= 0.293 Chirality : 0.046 0.172 3978 Planarity : 0.004 0.030 4476 Dihedral : 4.938 29.035 3426 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.19 % Favored : 93.62 % Rotamer: Outliers : 2.86 % Allowed : 16.59 % Favored : 80.55 % 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: 1.17 (0.16), residues: 1086 sheet: -0.44 (0.19), residues: 666 loop : -1.07 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 230 HIS 0.006 0.001 HIS A 228 PHE 0.011 0.001 PHE D 225 TYR 0.014 0.001 TYR C 318 ARG 0.002 0.000 ARG F 211 *********************** 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 246 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 167 time to evaluate : 2.721 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8444 (mtm) cc_final: 0.8174 (ttm) REVERT: F 150 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6432 (mpt-90) REVERT: F 154 GLN cc_start: 0.7801 (mm110) cc_final: 0.7509 (mt0) REVERT: F 163 ASP cc_start: 0.8428 (t70) cc_final: 0.8167 (t70) REVERT: F 281 LYS cc_start: 0.7603 (tttm) cc_final: 0.7237 (ptmt) REVERT: F 416 ASP cc_start: 0.7467 (t70) cc_final: 0.7229 (t70) REVERT: A 154 GLN cc_start: 0.7623 (mm110) cc_final: 0.7371 (mt0) REVERT: A 337 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 154 GLN cc_start: 0.7682 (mm110) cc_final: 0.7469 (mt0) REVERT: B 337 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8418 (mm) REVERT: C 154 GLN cc_start: 0.7691 (mm110) cc_final: 0.7401 (mt0) REVERT: C 281 LYS cc_start: 0.7460 (tttm) cc_final: 0.7167 (ptmt) REVERT: C 347 TYR cc_start: 0.8549 (m-80) cc_final: 0.8268 (m-80) REVERT: D 373 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7327 (p0) REVERT: E 150 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7022 (mpt-90) REVERT: E 154 GLN cc_start: 0.7768 (mm110) cc_final: 0.7522 (mt0) REVERT: E 373 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7395 (p0) REVERT: E 416 ASP cc_start: 0.7467 (t70) cc_final: 0.7244 (t0) REVERT: E 428 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8266 (mmtt) outliers start: 79 outliers final: 44 residues processed: 233 average time/residue: 1.3017 time to fit residues: 354.8557 Evaluate side-chains 209 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 240 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25890 Z= 0.220 Angle : 0.563 9.568 35118 Z= 0.294 Chirality : 0.046 0.181 3978 Planarity : 0.004 0.030 4476 Dihedral : 4.989 29.605 3426 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % Rotamer: Outliers : 2.53 % Allowed : 17.06 % Favored : 80.40 % 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: 1.25 (0.16), residues: 1080 sheet: -0.44 (0.19), residues: 666 loop : -1.11 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 230 HIS 0.007 0.001 HIS A 228 PHE 0.011 0.001 PHE D 225 TYR 0.012 0.001 TYR E 318 ARG 0.002 0.000 ARG D 130 *********************** 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 231 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 161 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7800 (mm110) cc_final: 0.7534 (mt0) REVERT: F 163 ASP cc_start: 0.8425 (t70) cc_final: 0.8191 (t70) REVERT: F 281 LYS cc_start: 0.7594 (tttm) cc_final: 0.7213 (ptmt) REVERT: F 322 GLU cc_start: 0.8381 (mp0) cc_final: 0.8109 (mp0) REVERT: A 154 GLN cc_start: 0.7631 (mm110) cc_final: 0.7401 (mt0) REVERT: A 337 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 154 GLN cc_start: 0.7683 (mm110) cc_final: 0.7477 (mt0) REVERT: B 337 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8395 (mm) REVERT: C 154 GLN cc_start: 0.7755 (mm110) cc_final: 0.7479 (mt0) REVERT: C 281 LYS cc_start: 0.7472 (tttm) cc_final: 0.7155 (ptmt) REVERT: C 347 TYR cc_start: 0.8547 (m-80) cc_final: 0.8296 (m-80) REVERT: D 373 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7320 (p0) REVERT: E 150 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7043 (mpt-90) REVERT: E 154 GLN cc_start: 0.7747 (mm110) cc_final: 0.7522 (mt0) REVERT: E 373 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7425 (p0) REVERT: E 416 ASP cc_start: 0.7465 (t70) cc_final: 0.7256 (t0) REVERT: E 428 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8321 (mmtm) outliers start: 70 outliers final: 45 residues processed: 220 average time/residue: 1.3046 time to fit residues: 334.6032 Evaluate side-chains 207 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 267 optimal weight: 0.5980 chunk 285 optimal weight: 0.0050 chunk 171 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25890 Z= 0.141 Angle : 0.520 11.389 35118 Z= 0.266 Chirality : 0.044 0.150 3978 Planarity : 0.003 0.029 4476 Dihedral : 4.733 30.626 3426 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 1.99 % Allowed : 17.64 % Favored : 80.37 % 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: -0.08 (0.15), residues: 3168 helix: 1.42 (0.17), residues: 1086 sheet: -0.41 (0.20), residues: 642 loop : -1.01 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 290 HIS 0.005 0.001 HIS B 228 PHE 0.008 0.001 PHE D 225 TYR 0.014 0.001 TYR E 318 ARG 0.002 0.000 ARG A 150 *********************** 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 221 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 2.862 Fit side-chains REVERT: F 150 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6566 (mpt-90) REVERT: F 154 GLN cc_start: 0.7697 (mm110) cc_final: 0.7411 (mt0) REVERT: F 163 ASP cc_start: 0.8437 (t70) cc_final: 0.8192 (t70) REVERT: F 281 LYS cc_start: 0.7596 (tttm) cc_final: 0.7231 (ptmt) REVERT: F 416 ASP cc_start: 0.7440 (t70) cc_final: 0.7208 (t70) REVERT: A 154 GLN cc_start: 0.7574 (mm110) cc_final: 0.7353 (mt0) REVERT: A 260 GLN cc_start: 0.7984 (tt0) cc_final: 0.7712 (tt0) REVERT: A 337 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 260 GLN cc_start: 0.7905 (tt0) cc_final: 0.7661 (tt0) REVERT: B 337 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8360 (mm) REVERT: C 154 GLN cc_start: 0.7611 (mm110) cc_final: 0.7358 (mt0) REVERT: C 281 LYS cc_start: 0.7432 (tttm) cc_final: 0.7123 (ptmt) REVERT: C 347 TYR cc_start: 0.8538 (m-80) cc_final: 0.8278 (m-80) REVERT: C 362 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7965 (pt) REVERT: D 373 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7276 (p0) REVERT: D 428 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8203 (mmtt) REVERT: E 150 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7167 (mpt-90) REVERT: E 154 GLN cc_start: 0.7732 (mm110) cc_final: 0.7532 (mt0) REVERT: E 373 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7374 (p0) REVERT: E 416 ASP cc_start: 0.7418 (t70) cc_final: 0.7046 (t0) REVERT: E 428 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8294 (mmtm) outliers start: 55 outliers final: 37 residues processed: 214 average time/residue: 1.3779 time to fit residues: 342.3521 Evaluate side-chains 206 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: