Starting phenix.real_space_refine on Mon Feb 19 17:47:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsy_35008/02_2024/8hsy_35008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsy_35008/02_2024/8hsy_35008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsy_35008/02_2024/8hsy_35008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsy_35008/02_2024/8hsy_35008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsy_35008/02_2024/8hsy_35008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsy_35008/02_2024/8hsy_35008.pdb" } resolution = 2.53 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= 0.000 sd= 0.078 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 "A ASP 46": "OD1" <-> "OD2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 418": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25320 Number of models: 1 Model: "" Number of chains: 6 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: "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: "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: "D" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "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 Time building chain proxies: 12.99, per 1000 atoms: 0.51 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: 9.91 Conformation dependent library (CDL) restraints added in 4.6 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 36.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.560A pdb=" N LEU A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (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: 3.765A 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 440 through 449 Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.553A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.560A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (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: 3.765A 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 440 through 449 Processing helix chain 'C' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.560A pdb=" N LEU B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (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: 3.765A 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 440 through 449 Processing helix chain 'B' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.560A pdb=" N LEU D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (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: 3.765A 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 440 through 449 Processing helix chain 'D' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.553A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.559A pdb=" N LEU E 124 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.799A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.892A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (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: 3.765A 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 440 through 449 Processing helix chain 'E' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.552A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.559A pdb=" N LEU F 124 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.800A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.893A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (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: 3.765A 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 440 through 449 Processing helix chain 'F' and resid 483 through 494 removed outlier: 4.099A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN A 243 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER A 266 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 315 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 171 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN C 243 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER C 266 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 315 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 171 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AB1, first strand: chain 'C' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN B 243 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER B 266 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 315 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 171 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.348A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB6, first strand: chain 'B' and resid 453 through 461 removed outlier: 6.507A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN D 243 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER D 266 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 315 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 171 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.348A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 37 through 40 removed outlier: 3.581A pdb=" N GLN E 243 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 266 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 315 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.952A pdb=" N THR E 65 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU E 115 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA E 67 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS E 117 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET E 69 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 171 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 37 through 40 removed outlier: 3.580A pdb=" N GLN F 243 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER F 266 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE F 315 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.953A pdb=" N THR F 65 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU F 115 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA F 67 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS F 117 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET F 69 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 171 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.347A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 461 removed outlier: 6.508A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.45 Time building geometry restraints manager: 10.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4266 1.31 - 1.43: 6527 1.43 - 1.56: 14905 1.56 - 1.68: 0 1.68 - 1.81: 192 Bond restraints: 25890 Sorted by residual: bond pdb=" C ASN E 368 " pdb=" O ASN E 368 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C ASN A 368 " pdb=" O ASN A 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C ASN C 368 " pdb=" O ASN C 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C ASN F 368 " pdb=" O ASN F 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C ASN D 368 " pdb=" O ASN D 368 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.30e-02 5.92e+03 1.56e+01 ... (remaining 25885 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 756 106.51 - 113.38: 14227 113.38 - 120.25: 9145 120.25 - 127.12: 10672 127.12 - 133.99: 318 Bond angle restraints: 35118 Sorted by residual: angle pdb=" N MET C 367 " pdb=" CA MET C 367 " pdb=" C MET C 367 " ideal model delta sigma weight residual 111.02 121.27 -10.25 1.25e+00 6.40e-01 6.72e+01 angle pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" C MET B 367 " ideal model delta sigma weight residual 111.02 121.26 -10.24 1.25e+00 6.40e-01 6.71e+01 angle pdb=" N MET F 367 " pdb=" CA MET F 367 " pdb=" C MET F 367 " ideal model delta sigma weight residual 111.02 121.25 -10.23 1.25e+00 6.40e-01 6.70e+01 angle pdb=" N MET E 367 " pdb=" CA MET E 367 " pdb=" C MET E 367 " ideal model delta sigma weight residual 111.02 121.24 -10.22 1.25e+00 6.40e-01 6.68e+01 angle pdb=" N MET A 367 " pdb=" CA MET A 367 " pdb=" C MET A 367 " ideal model delta sigma weight residual 111.02 121.23 -10.21 1.25e+00 6.40e-01 6.67e+01 ... (remaining 35113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 13796 17.30 - 34.59: 1228 34.59 - 51.89: 390 51.89 - 69.18: 78 69.18 - 86.48: 30 Dihedral angle restraints: 15522 sinusoidal: 6252 harmonic: 9270 Sorted by residual: dihedral pdb=" C MET B 367 " pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" CB MET B 367 " ideal model delta harmonic sigma weight residual -122.60 -132.28 9.68 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C MET C 367 " pdb=" N MET C 367 " pdb=" CA MET C 367 " pdb=" CB MET C 367 " ideal model delta harmonic sigma weight residual -122.60 -132.27 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C MET E 367 " pdb=" N MET E 367 " pdb=" CA MET E 367 " pdb=" CB MET E 367 " ideal model delta harmonic sigma weight residual -122.60 -132.25 9.65 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 15519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3840 0.113 - 0.225: 120 0.225 - 0.338: 12 0.338 - 0.450: 0 0.450 - 0.563: 6 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA MET C 367 " pdb=" N MET C 367 " pdb=" C MET C 367 " pdb=" CB MET C 367 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CA MET E 367 " pdb=" N MET E 367 " pdb=" C MET E 367 " pdb=" CB MET E 367 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 3975 not shown) Planarity restraints: 4476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 340 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ASP B 340 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP B 340 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL B 341 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 340 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ASP C 340 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP C 340 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 341 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 340 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C ASP D 340 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 340 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 341 " -0.014 2.00e-02 2.50e+03 ... (remaining 4473 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 618 2.70 - 3.25: 24383 3.25 - 3.80: 40376 3.80 - 4.35: 55483 4.35 - 4.90: 89973 Nonbonded interactions: 210833 Sorted by model distance: nonbonded pdb=" OD1 ASP C 416 " pdb=" N ASP C 417 " model vdw 2.153 2.520 nonbonded pdb=" OD1 ASP B 416 " pdb=" N ASP B 417 " model vdw 2.153 2.520 nonbonded pdb=" OD1 ASP A 416 " pdb=" N ASP A 417 " model vdw 2.153 2.520 nonbonded pdb=" OD1 ASP E 416 " pdb=" N ASP E 417 " model vdw 2.153 2.520 nonbonded pdb=" OD1 ASP D 416 " pdb=" N ASP D 417 " model vdw 2.153 2.520 ... (remaining 210828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.490 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: 8.470 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 69.230 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.160 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.004 0.052 25890 Z= 0.258 Angle : 0.707 10.246 35118 Z= 0.440 Chirality : 0.055 0.563 3978 Planarity : 0.004 0.037 4476 Dihedral : 15.459 86.476 9558 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.25 % Favored : 93.56 % Rotamer: Outliers : 0.80 % Allowed : 12.87 % Favored : 86.33 % 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: -0.75 (0.15), residues: 3168 helix: 0.67 (0.16), residues: 1062 sheet: -0.73 (0.20), residues: 612 loop : -1.21 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 290 HIS 0.003 0.001 HIS F 45 PHE 0.011 0.001 PHE E 225 TYR 0.010 0.001 TYR C 148 ARG 0.005 0.000 ARG F 130 *********************** 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 269 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 247 time to evaluate : 2.943 Fit side-chains REVERT: C 364 ASP cc_start: 0.7111 (p0) cc_final: 0.6665 (p0) REVERT: D 92 MET cc_start: 0.8890 (mtm) cc_final: 0.8503 (mtp) REVERT: E 92 MET cc_start: 0.8904 (mtm) cc_final: 0.8558 (mtp) outliers start: 22 outliers final: 1 residues processed: 258 average time/residue: 1.4298 time to fit residues: 423.6407 Evaluate side-chains 203 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU 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: 7.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 243 GLN A 368 ASN C 17 ASN C 108 HIS C 189 HIS C 243 GLN C 368 ASN B 17 ASN B 243 GLN B 368 ASN D 108 HIS D 243 GLN D 368 ASN E 108 HIS E 243 GLN E 368 ASN F 17 ASN F 108 HIS F 189 HIS F 243 GLN F 368 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 25890 Z= 0.468 Angle : 0.723 7.530 35118 Z= 0.394 Chirality : 0.054 0.175 3978 Planarity : 0.006 0.054 4476 Dihedral : 5.964 48.844 3429 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.17 % Favored : 92.65 % Rotamer: Outliers : 3.69 % Allowed : 12.83 % Favored : 83.48 % 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: -0.74 (0.14), residues: 3168 helix: 0.79 (0.16), residues: 1080 sheet: -0.60 (0.20), residues: 570 loop : -1.39 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 230 HIS 0.009 0.002 HIS F 45 PHE 0.018 0.002 PHE E 225 TYR 0.019 0.003 TYR C 318 ARG 0.005 0.001 ARG F 211 *********************** 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 302 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 200 time to evaluate : 3.224 Fit side-chains REVERT: A 365 GLU cc_start: 0.7102 (mp0) cc_final: 0.6827 (mp0) REVERT: A 442 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5797 (pm20) REVERT: A 453 VAL cc_start: 0.2593 (OUTLIER) cc_final: 0.2357 (p) REVERT: A 528 LEU cc_start: 0.6971 (mt) cc_final: 0.6746 (mm) REVERT: C 331 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6242 (mp10) REVERT: C 364 ASP cc_start: 0.7848 (p0) cc_final: 0.7584 (p0) REVERT: C 453 VAL cc_start: 0.2757 (OUTLIER) cc_final: 0.2406 (p) REVERT: B 28 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 331 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: B 365 GLU cc_start: 0.7082 (mp0) cc_final: 0.6837 (mp0) REVERT: B 453 VAL cc_start: 0.2849 (OUTLIER) cc_final: 0.2513 (p) REVERT: D 119 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: D 331 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.6426 (mp10) REVERT: D 453 VAL cc_start: 0.2833 (OUTLIER) cc_final: 0.2492 (p) REVERT: E 119 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: E 154 GLN cc_start: 0.8102 (mt0) cc_final: 0.7824 (mt0) REVERT: E 331 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6498 (mp10) REVERT: E 453 VAL cc_start: 0.2630 (OUTLIER) cc_final: 0.2370 (p) REVERT: F 331 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6353 (mp10) REVERT: F 364 ASP cc_start: 0.7817 (p0) cc_final: 0.7408 (p0) REVERT: F 453 VAL cc_start: 0.3186 (OUTLIER) cc_final: 0.2819 (p) outliers start: 102 outliers final: 26 residues processed: 266 average time/residue: 1.3456 time to fit residues: 416.2006 Evaluate side-chains 233 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 0.0270 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 312 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 overall best weight: 0.9854 ------------------------------------------------------------------------------- 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: 0.8490 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25890 Z= 0.184 Angle : 0.560 6.431 35118 Z= 0.302 Chirality : 0.047 0.147 3978 Planarity : 0.004 0.046 4476 Dihedral : 5.505 46.742 3429 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.38 % Favored : 93.43 % Rotamer: Outliers : 2.86 % Allowed : 13.81 % Favored : 83.33 % 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: -0.50 (0.14), residues: 3168 helix: 1.17 (0.16), residues: 1080 sheet: -0.58 (0.20), residues: 582 loop : -1.35 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS B 228 PHE 0.015 0.001 PHE E 225 TYR 0.010 0.001 TYR F 148 ARG 0.003 0.000 ARG D 130 *********************** 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 282 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 203 time to evaluate : 3.723 Fit side-chains REVERT: A 337 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8432 (mt) REVERT: A 442 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5786 (pm20) REVERT: A 453 VAL cc_start: 0.2971 (OUTLIER) cc_final: 0.2751 (p) REVERT: A 528 LEU cc_start: 0.6911 (mt) cc_final: 0.6647 (mm) REVERT: B 331 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: B 337 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8466 (mt) REVERT: D 119 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: D 331 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6261 (mp10) REVERT: D 337 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8383 (mt) REVERT: E 337 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (mt) REVERT: F 331 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6513 (mp10) REVERT: F 364 ASP cc_start: 0.7643 (p0) cc_final: 0.7423 (p0) outliers start: 79 outliers final: 27 residues processed: 260 average time/residue: 1.4385 time to fit residues: 440.7694 Evaluate side-chains 222 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 290 optimal weight: 0.6980 chunk 307 optimal weight: 0.0870 chunk 151 optimal weight: 20.0000 chunk 275 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25890 Z= 0.182 Angle : 0.544 6.511 35118 Z= 0.293 Chirality : 0.046 0.145 3978 Planarity : 0.004 0.046 4476 Dihedral : 5.260 31.690 3426 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 3.15 % Allowed : 14.06 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3168 helix: 1.33 (0.16), residues: 1080 sheet: -0.58 (0.20), residues: 540 loop : -1.30 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 402 HIS 0.003 0.001 HIS D 45 PHE 0.014 0.001 PHE E 225 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG B 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 276 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 189 time to evaluate : 2.719 Fit side-chains REVERT: A 337 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 442 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5793 (pm20) REVERT: A 461 MET cc_start: 0.3650 (pmt) cc_final: 0.2788 (mpp) REVERT: C 61 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8157 (mttp) REVERT: C 331 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: C 362 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8372 (tp) REVERT: C 453 VAL cc_start: 0.2755 (OUTLIER) cc_final: 0.2414 (p) REVERT: B 331 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6562 (mp10) REVERT: B 337 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 453 VAL cc_start: 0.2950 (OUTLIER) cc_final: 0.2653 (p) REVERT: D 337 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8374 (mt) REVERT: D 453 VAL cc_start: 0.2600 (OUTLIER) cc_final: 0.2338 (p) REVERT: E 119 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: E 337 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8352 (mt) REVERT: E 453 VAL cc_start: 0.2872 (OUTLIER) cc_final: 0.2625 (p) REVERT: F 42 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8463 (ttpt) REVERT: F 331 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6408 (mp10) REVERT: F 453 VAL cc_start: 0.2748 (OUTLIER) cc_final: 0.2420 (p) outliers start: 87 outliers final: 31 residues processed: 257 average time/residue: 1.2508 time to fit residues: 377.1407 Evaluate side-chains 238 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 228 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 262 optimal weight: 0.0870 chunk 212 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25890 Z= 0.151 Angle : 0.518 6.224 35118 Z= 0.278 Chirality : 0.046 0.151 3978 Planarity : 0.004 0.043 4476 Dihedral : 5.041 27.948 3426 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.22 % Favored : 93.59 % Rotamer: Outliers : 3.11 % Allowed : 14.82 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3168 helix: 1.51 (0.16), residues: 1080 sheet: -0.53 (0.21), residues: 528 loop : -1.23 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 290 HIS 0.003 0.001 HIS C 414 PHE 0.014 0.001 PHE D 225 TYR 0.009 0.001 TYR F 148 ARG 0.002 0.000 ARG C 130 *********************** 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 284 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 198 time to evaluate : 3.036 Fit side-chains REVERT: A 119 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: A 337 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8385 (mt) REVERT: A 442 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5812 (pm20) REVERT: C 61 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: C 453 VAL cc_start: 0.2743 (OUTLIER) cc_final: 0.2408 (p) REVERT: B 331 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6355 (mp10) REVERT: B 337 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 453 VAL cc_start: 0.3020 (OUTLIER) cc_final: 0.2719 (p) REVERT: D 92 MET cc_start: 0.8998 (mtm) cc_final: 0.8688 (mtp) REVERT: D 453 VAL cc_start: 0.2599 (OUTLIER) cc_final: 0.2353 (p) REVERT: E 92 MET cc_start: 0.8977 (mtm) cc_final: 0.8770 (mtp) REVERT: E 331 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: E 453 VAL cc_start: 0.2832 (OUTLIER) cc_final: 0.2593 (p) REVERT: F 42 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8408 (ttpt) REVERT: F 130 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7830 (mtm180) REVERT: F 453 VAL cc_start: 0.2796 (OUTLIER) cc_final: 0.2474 (p) outliers start: 86 outliers final: 31 residues processed: 261 average time/residue: 1.3890 time to fit residues: 420.9200 Evaluate side-chains 238 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 8.9990 chunk 276 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 0.4980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25890 Z= 0.151 Angle : 0.517 6.187 35118 Z= 0.277 Chirality : 0.046 0.161 3978 Planarity : 0.004 0.042 4476 Dihedral : 4.965 25.202 3426 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.34 % Rotamer: Outliers : 2.75 % Allowed : 15.08 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3168 helix: 1.58 (0.16), residues: 1080 sheet: -0.42 (0.21), residues: 540 loop : -1.20 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 402 HIS 0.003 0.001 HIS E 414 PHE 0.013 0.001 PHE E 225 TYR 0.009 0.001 TYR E 245 ARG 0.002 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 273 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 197 time to evaluate : 3.146 Fit side-chains REVERT: A 337 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8375 (mt) REVERT: A 442 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5801 (pm20) REVERT: A 461 MET cc_start: 0.3581 (pmt) cc_final: 0.2718 (mpp) REVERT: C 61 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: C 453 VAL cc_start: 0.2745 (OUTLIER) cc_final: 0.2405 (p) REVERT: B 331 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6284 (mp10) REVERT: B 337 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8394 (mt) REVERT: B 453 VAL cc_start: 0.3015 (OUTLIER) cc_final: 0.2708 (p) REVERT: D 92 MET cc_start: 0.8988 (mtm) cc_final: 0.8662 (mtp) REVERT: D 453 VAL cc_start: 0.2598 (OUTLIER) cc_final: 0.2344 (p) REVERT: E 92 MET cc_start: 0.8960 (mtm) cc_final: 0.8742 (mtp) REVERT: E 331 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.5701 (mp10) REVERT: E 453 VAL cc_start: 0.2872 (OUTLIER) cc_final: 0.2631 (p) REVERT: F 42 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8409 (ttpt) REVERT: F 130 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7875 (mtm180) REVERT: F 453 VAL cc_start: 0.2784 (OUTLIER) cc_final: 0.2460 (p) outliers start: 76 outliers final: 29 residues processed: 258 average time/residue: 1.3522 time to fit residues: 406.7455 Evaluate side-chains 236 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL 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: 4.9990 chunk 175 optimal weight: 5.9990 chunk 224 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 259 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 0.1980 chunk 191 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1846 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= 0.136 Angle : 0.503 6.086 35118 Z= 0.268 Chirality : 0.045 0.172 3978 Planarity : 0.004 0.040 4476 Dihedral : 4.796 22.014 3426 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.22 % Favored : 93.59 % Rotamer: Outliers : 2.57 % Allowed : 15.44 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3168 helix: 1.67 (0.16), residues: 1086 sheet: -0.17 (0.22), residues: 504 loop : -1.10 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.003 0.001 HIS C 414 PHE 0.013 0.001 PHE E 225 TYR 0.009 0.001 TYR A 148 ARG 0.002 0.000 ARG C 130 *********************** 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 272 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 201 time to evaluate : 3.299 Fit side-chains REVERT: A 337 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 442 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5828 (pm20) REVERT: A 461 MET cc_start: 0.3615 (pmt) cc_final: 0.2693 (mpp) REVERT: C 61 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8136 (mttp) REVERT: C 453 VAL cc_start: 0.2761 (OUTLIER) cc_final: 0.2427 (p) REVERT: B 337 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 453 VAL cc_start: 0.2993 (OUTLIER) cc_final: 0.2691 (p) REVERT: B 461 MET cc_start: 0.3680 (pmt) cc_final: 0.2800 (mpp) REVERT: D 92 MET cc_start: 0.8936 (mtm) cc_final: 0.8683 (mtp) REVERT: D 453 VAL cc_start: 0.2658 (OUTLIER) cc_final: 0.2351 (p) REVERT: D 506 LEU cc_start: 0.3098 (OUTLIER) cc_final: 0.2602 (pp) REVERT: E 92 MET cc_start: 0.8894 (mtm) cc_final: 0.8654 (mtp) REVERT: E 453 VAL cc_start: 0.2861 (OUTLIER) cc_final: 0.2626 (p) REVERT: F 42 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8393 (ttpt) REVERT: F 119 GLU cc_start: 0.7357 (pt0) cc_final: 0.7130 (pt0) REVERT: F 130 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7880 (mtm180) REVERT: F 453 VAL cc_start: 0.2721 (OUTLIER) cc_final: 0.2397 (p) outliers start: 71 outliers final: 30 residues processed: 251 average time/residue: 1.2932 time to fit residues: 379.3744 Evaluate side-chains 236 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 28 optimal weight: 0.4980 chunk 240 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8490 moved from start: 0.1938 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= 0.227 Angle : 0.565 6.349 35118 Z= 0.304 Chirality : 0.047 0.167 3978 Planarity : 0.004 0.044 4476 Dihedral : 5.056 19.985 3426 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 2.42 % Allowed : 15.80 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3168 helix: 1.53 (0.16), residues: 1080 sheet: -0.16 (0.21), residues: 516 loop : -1.20 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 466 HIS 0.004 0.001 HIS B 228 PHE 0.013 0.001 PHE E 225 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 192 time to evaluate : 2.788 Fit side-chains REVERT: A 337 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8391 (mt) REVERT: A 461 MET cc_start: 0.3598 (pmt) cc_final: 0.2811 (mpp) REVERT: A 506 LEU cc_start: 0.2801 (OUTLIER) cc_final: 0.2498 (pp) REVERT: C 61 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: C 362 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (tp) REVERT: C 453 VAL cc_start: 0.2828 (OUTLIER) cc_final: 0.2481 (p) REVERT: B 119 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7057 (pt0) REVERT: B 337 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 453 VAL cc_start: 0.3091 (OUTLIER) cc_final: 0.2792 (p) REVERT: B 506 LEU cc_start: 0.2800 (OUTLIER) cc_final: 0.2466 (pp) REVERT: D 453 VAL cc_start: 0.2731 (OUTLIER) cc_final: 0.2434 (p) REVERT: D 506 LEU cc_start: 0.2945 (OUTLIER) cc_final: 0.2521 (pp) REVERT: E 453 VAL cc_start: 0.2971 (OUTLIER) cc_final: 0.2736 (p) REVERT: F 42 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8493 (ttpt) REVERT: F 119 GLU cc_start: 0.7485 (pt0) cc_final: 0.7269 (pt0) REVERT: F 130 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8015 (mtm180) REVERT: F 453 VAL cc_start: 0.2789 (OUTLIER) cc_final: 0.2447 (p) outliers start: 67 outliers final: 34 residues processed: 245 average time/residue: 1.3157 time to fit residues: 377.0670 Evaluate side-chains 238 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET 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 363 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 222 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 363 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU 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: 2.9990 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8511 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25890 Z= 0.278 Angle : 0.598 6.792 35118 Z= 0.323 Chirality : 0.049 0.166 3978 Planarity : 0.004 0.044 4476 Dihedral : 5.291 21.015 3426 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.98 % Favored : 92.83 % Rotamer: Outliers : 2.42 % Allowed : 15.84 % 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: -0.28 (0.14), residues: 3168 helix: 1.34 (0.16), residues: 1080 sheet: -0.28 (0.21), residues: 516 loop : -1.27 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 466 HIS 0.004 0.001 HIS E 45 PHE 0.015 0.002 PHE E 225 TYR 0.011 0.002 TYR E 245 ARG 0.003 0.000 ARG C 47 *********************** 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 250 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 183 time to evaluate : 3.345 Fit side-chains REVERT: A 337 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8466 (mt) REVERT: A 461 MET cc_start: 0.3655 (pmt) cc_final: 0.2911 (mpp) REVERT: C 61 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: C 362 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8475 (tp) REVERT: C 453 VAL cc_start: 0.2807 (OUTLIER) cc_final: 0.2468 (p) REVERT: B 119 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: B 337 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8448 (mt) REVERT: B 453 VAL cc_start: 0.2942 (OUTLIER) cc_final: 0.2675 (p) REVERT: D 418 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: D 506 LEU cc_start: 0.3207 (OUTLIER) cc_final: 0.2737 (pp) REVERT: F 119 GLU cc_start: 0.7515 (pt0) cc_final: 0.7292 (pt0) REVERT: F 130 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8077 (mtm180) REVERT: F 453 VAL cc_start: 0.2722 (OUTLIER) cc_final: 0.2364 (p) outliers start: 67 outliers final: 35 residues processed: 237 average time/residue: 1.3379 time to fit residues: 371.2299 Evaluate side-chains 231 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET 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 363 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 222 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 363 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.0270 chunk 302 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- 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: 0.8492 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25890 Z= 0.203 Angle : 0.563 8.421 35118 Z= 0.302 Chirality : 0.047 0.195 3978 Planarity : 0.004 0.043 4476 Dihedral : 5.164 20.860 3426 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.01 % Favored : 92.80 % Rotamer: Outliers : 1.92 % Allowed : 16.27 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3168 helix: 1.41 (0.16), residues: 1080 sheet: -0.11 (0.21), residues: 558 loop : -1.28 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 466 HIS 0.003 0.001 HIS C 267 PHE 0.014 0.001 PHE D 225 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG C 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 182 time to evaluate : 3.201 Fit side-chains REVERT: A 337 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 418 GLU cc_start: 0.6580 (pt0) cc_final: 0.6215 (tt0) REVERT: A 461 MET cc_start: 0.3612 (pmt) cc_final: 0.2885 (mpp) REVERT: A 506 LEU cc_start: 0.2733 (OUTLIER) cc_final: 0.2433 (pp) REVERT: C 61 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: C 362 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8407 (tp) REVERT: C 453 VAL cc_start: 0.2808 (OUTLIER) cc_final: 0.2472 (p) REVERT: B 119 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: B 337 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 453 VAL cc_start: 0.2953 (OUTLIER) cc_final: 0.2685 (p) REVERT: D 418 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: D 506 LEU cc_start: 0.3163 (OUTLIER) cc_final: 0.2691 (pp) REVERT: F 119 GLU cc_start: 0.7476 (pt0) cc_final: 0.7250 (pt0) REVERT: F 130 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8035 (mtm180) REVERT: F 453 VAL cc_start: 0.2746 (OUTLIER) cc_final: 0.2404 (p) outliers start: 53 outliers final: 33 residues processed: 224 average time/residue: 1.3719 time to fit residues: 358.8427 Evaluate side-chains 227 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 222 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 363 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.9990 chunk 268 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117227 restraints weight = 30228.305| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.82 r_work: 0.3225 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25890 Z= 0.241 Angle : 0.580 8.351 35118 Z= 0.312 Chirality : 0.048 0.279 3978 Planarity : 0.004 0.044 4476 Dihedral : 5.214 21.282 3426 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.42 % Favored : 92.39 % Rotamer: Outliers : 1.99 % Allowed : 16.38 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3168 helix: 1.20 (0.16), residues: 1116 sheet: -0.11 (0.21), residues: 558 loop : -1.38 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 466 HIS 0.004 0.001 HIS E 45 PHE 0.014 0.001 PHE E 225 TYR 0.013 0.001 TYR E 245 ARG 0.002 0.000 ARG F 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7695.10 seconds wall clock time: 139 minutes 7.33 seconds (8347.33 seconds total)