Starting phenix.real_space_refine on Mon Mar 11 05:25:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/03_2024/8bmd_16118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/03_2024/8bmd_16118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/03_2024/8bmd_16118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/03_2024/8bmd_16118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/03_2024/8bmd_16118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/03_2024/8bmd_16118_updated.pdb" } resolution = 2.8 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= 0.006 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: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 280 5.16 5 C 33628 2.51 5 N 9380 2.21 5 O 12174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 224": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 224": "OD1" <-> "OD2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 52": "OD1" <-> "OD2" Residue "I ASP 224": "OD1" <-> "OD2" Residue "I GLU 257": "OE1" <-> "OE2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 257": "OE1" <-> "OE2" Residue "M ASP 435": "OD1" <-> "OD2" Residue "M ASP 473": "OD1" <-> "OD2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 435": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55532 Number of models: 1 Model: "" Number of chains: 42 Chain: "G" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "F" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "I" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "J" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "M" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG A 601 " occ=0.00 residue: pdb="MG MG B 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG D 601 " occ=0.00 residue: pdb="MG MG E 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG H 601 " occ=0.00 residue: pdb="MG MG I 601 " occ=0.00 residue: pdb="MG MG J 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG L 601 " occ=0.00 ... (remaining 2 not shown) Time building chain proxies: 21.61, per 1000 atoms: 0.39 Number of scatterers: 55532 At special positions: 0 Unit cell: (150.72, 152.64, 162.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 280 16.00 P 42 15.00 Mg 14 11.99 O 12174 8.00 N 9380 7.00 C 33628 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: 17.07 Conformation dependent library (CDL) restraints added in 7.3 seconds 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 276 helices and 109 sheets defined 52.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.66 Creating SS restraints... Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.905A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.843A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 138 through 141 No H-bonds generated for 'chain 'G' and resid 138 through 141' Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 156 through 168 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 231 through 243 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 260 through 264 Processing helix chain 'G' and resid 283 through 296 Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 359 through 373 Processing helix chain 'G' and resid 386 through 409 Processing helix chain 'G' and resid 417 through 425 Processing helix chain 'G' and resid 434 through 458 removed outlier: 3.814A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.955A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 30 removed outlier: 4.808A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.943A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 434 through 458 removed outlier: 3.795A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.925A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 removed outlier: 4.758A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 65 through 84 removed outlier: 4.051A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 108 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 156 through 168 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 231 through 242 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 409 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 434 through 457 removed outlier: 3.911A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.930A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 30 removed outlier: 4.769A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 84 removed outlier: 4.044A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 108 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 156 through 168 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 434 through 457 removed outlier: 3.821A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.894A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 removed outlier: 4.911A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.823A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 266 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 417 through 425 Processing helix chain 'D' and resid 434 through 457 removed outlier: 3.797A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.910A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 30 removed outlier: 4.793A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.969A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 108 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 156 through 166 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 230 through 241 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 266 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 374 Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 434 through 458 removed outlier: 3.879A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.865A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 removed outlier: 4.835A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.834A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 108 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 234 through 243 Processing helix chain 'F' and resid 260 through 266 Processing helix chain 'F' and resid 283 through 296 Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 359 through 374 Processing helix chain 'F' and resid 386 through 409 Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'F' and resid 434 through 458 removed outlier: 3.746A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.924A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 30 removed outlier: 4.797A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.869A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 138 through 141 No H-bonds generated for 'chain 'H' and resid 138 through 141' Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'H' and resid 156 through 168 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 230 through 241 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 260 through 266 Processing helix chain 'H' and resid 283 through 296 Processing helix chain 'H' and resid 309 through 311 No H-bonds generated for 'chain 'H' and resid 309 through 311' Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 359 through 374 Processing helix chain 'H' and resid 386 through 409 Processing helix chain 'H' and resid 417 through 425 Processing helix chain 'H' and resid 434 through 457 removed outlier: 3.795A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.937A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 30 removed outlier: 4.780A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.972A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 156 through 168 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 231 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 260 through 266 Processing helix chain 'I' and resid 283 through 296 Processing helix chain 'I' and resid 309 through 311 No H-bonds generated for 'chain 'I' and resid 309 through 311' Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 373 Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 425 Processing helix chain 'I' and resid 434 through 457 removed outlier: 3.791A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.956A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 30 removed outlier: 4.819A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 84 removed outlier: 3.826A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 138 through 141 No H-bonds generated for 'chain 'J' and resid 138 through 141' Processing helix chain 'J' and resid 144 through 151 Processing helix chain 'J' and resid 156 through 168 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 230 through 241 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 260 through 266 Processing helix chain 'J' and resid 283 through 296 Processing helix chain 'J' and resid 309 through 311 No H-bonds generated for 'chain 'J' and resid 309 through 311' Processing helix chain 'J' and resid 339 through 355 Processing helix chain 'J' and resid 359 through 374 Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 417 through 425 Processing helix chain 'J' and resid 434 through 458 removed outlier: 3.735A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 462 through 471 Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.947A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 30 removed outlier: 4.836A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 85 removed outlier: 3.938A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 138 through 141 No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'K' and resid 156 through 168 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 234 through 243 Processing helix chain 'K' and resid 261 through 264 No H-bonds generated for 'chain 'K' and resid 261 through 264' Processing helix chain 'K' and resid 283 through 296 Processing helix chain 'K' and resid 309 through 311 No H-bonds generated for 'chain 'K' and resid 309 through 311' Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 417 through 426 Processing helix chain 'K' and resid 434 through 458 removed outlier: 3.878A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA K 449 " --> pdb=" O ARG K 445 " (cutoff:3.500A) Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.898A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 4.915A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 84 removed outlier: 3.805A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 138 through 141 No H-bonds generated for 'chain 'L' and resid 138 through 141' Processing helix chain 'L' and resid 144 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 234 through 241 Processing helix chain 'L' and resid 260 through 266 Processing helix chain 'L' and resid 283 through 296 Processing helix chain 'L' and resid 309 through 311 No H-bonds generated for 'chain 'L' and resid 309 through 311' Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 374 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 425 Processing helix chain 'L' and resid 434 through 457 removed outlier: 3.789A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.891A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 30 removed outlier: 4.798A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.978A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 138 through 141 No H-bonds generated for 'chain 'M' and resid 138 through 141' Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 156 through 168 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 231 through 241 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 261 through 266 Processing helix chain 'M' and resid 283 through 296 Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'M' and resid 339 through 355 Processing helix chain 'M' and resid 359 through 374 Processing helix chain 'M' and resid 386 through 409 Processing helix chain 'M' and resid 417 through 425 Processing helix chain 'M' and resid 434 through 457 removed outlier: 3.821A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA M 449 " --> pdb=" O ARG M 445 " (cutoff:3.500A) Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.910A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 30 removed outlier: 4.779A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 84 removed outlier: 3.873A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 138 through 141 No H-bonds generated for 'chain 'N' and resid 138 through 141' Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 156 through 168 Processing helix chain 'N' and resid 231 through 241 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 260 through 266 Processing helix chain 'N' and resid 283 through 296 Processing helix chain 'N' and resid 339 through 355 Processing helix chain 'N' and resid 359 through 374 Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 426 Processing helix chain 'N' and resid 434 through 457 removed outlier: 3.930A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'G' and resid 213 through 216 Processing sheet with id= F, first strand: chain 'G' and resid 219 through 222 removed outlier: 7.020A pdb=" N ALA G 274 " --> pdb=" O ILE G 249 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= H, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= I, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= K, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= L, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= M, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= N, first strand: chain 'A' and resid 219 through 222 removed outlier: 7.068A pdb=" N ALA A 274 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= P, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= Q, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= R, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= S, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= T, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= U, first strand: chain 'B' and resid 213 through 216 Processing sheet with id= V, first strand: chain 'B' and resid 219 through 221 Processing sheet with id= W, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= X, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= Y, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= AB, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AC, first strand: chain 'C' and resid 213 through 216 Processing sheet with id= AD, first strand: chain 'C' and resid 219 through 222 removed outlier: 7.270A pdb=" N ALA C 274 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AF, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= AG, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AH, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AJ, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AK, first strand: chain 'D' and resid 213 through 216 Processing sheet with id= AL, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AM, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AN, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AO, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AP, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AQ, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AR, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AS, first strand: chain 'E' and resid 213 through 216 Processing sheet with id= AT, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AU, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AV, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AW, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AX, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AY, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AZ, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= BA, first strand: chain 'F' and resid 213 through 216 Processing sheet with id= BB, first strand: chain 'F' and resid 219 through 222 removed outlier: 6.859A pdb=" N ALA F 274 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= BD, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= BE, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= BI, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= BJ, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BL, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BM, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BN, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BO, first strand: chain 'I' and resid 193 through 195 Processing sheet with id= BP, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= BQ, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BR, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BS, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BT, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BU, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BV, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BW, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.508A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'J' and resid 219 through 222 Processing sheet with id= BY, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BZ, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= CA, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= CB, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= CC, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= CD, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= CE, first strand: chain 'K' and resid 213 through 216 Processing sheet with id= CF, first strand: chain 'K' and resid 219 through 222 removed outlier: 7.022A pdb=" N ALA K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= CH, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= CI, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CJ, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CK, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CL, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CM, first strand: chain 'L' and resid 219 through 222 removed outlier: 6.771A pdb=" N ALA L 274 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA L 251 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL L 276 " --> pdb=" O ALA L 251 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CO, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CP, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CQ, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CR, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CS, first strand: chain 'M' and resid 193 through 195 removed outlier: 4.232A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'M' and resid 213 through 216 Processing sheet with id= CU, first strand: chain 'M' and resid 219 through 222 removed outlier: 6.997A pdb=" N ALA M 274 " --> pdb=" O ILE M 249 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CW, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CX, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= CY, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CZ, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= DA, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= DB, first strand: chain 'N' and resid 213 through 216 removed outlier: 3.505A pdb=" N VAL N 323 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= DD, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= DE, first strand: chain 'N' and resid 476 through 479 3122 hydrogen bonds defined for protein. 9033 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: 19.15 Time building geometry restraints manager: 18.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18825 1.34 - 1.46: 9552 1.46 - 1.58: 25804 1.58 - 1.70: 27 1.70 - 1.82: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" CG1 ILE A 353 " pdb=" CD1 ILE A 353 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CB VAL L 74 " pdb=" CG2 VAL L 74 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 bond pdb=" SD MET H 520 " pdb=" CE MET H 520 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.16e+00 bond pdb=" C LEU E 494 " pdb=" N ASP E 495 " ideal model delta sigma weight residual 1.331 1.301 0.030 2.07e-02 2.33e+03 2.14e+00 bond pdb=" CA MET J 267 " pdb=" CB MET J 267 " ideal model delta sigma weight residual 1.534 1.568 -0.034 2.47e-02 1.64e+03 1.86e+00 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 96.93 - 105.53: 898 105.53 - 114.14: 33521 114.14 - 122.75: 34887 122.75 - 131.35: 4642 131.35 - 139.96: 42 Bond angle restraints: 73990 Sorted by residual: angle pdb=" N GLY M 192 " pdb=" CA GLY M 192 " pdb=" C GLY M 192 " ideal model delta sigma weight residual 113.18 126.16 -12.98 2.37e+00 1.78e-01 3.00e+01 angle pdb=" CA MET E 233 " pdb=" CB MET E 233 " pdb=" CG MET E 233 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CB MET L 267 " pdb=" CG MET L 267 " pdb=" SD MET L 267 " ideal model delta sigma weight residual 112.70 98.55 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CB MET K 233 " pdb=" CG MET K 233 " pdb=" SD MET K 233 " ideal model delta sigma weight residual 112.70 126.68 -13.98 3.00e+00 1.11e-01 2.17e+01 angle pdb=" CB MET C 307 " pdb=" CG MET C 307 " pdb=" SD MET C 307 " ideal model delta sigma weight residual 112.70 125.09 -12.39 3.00e+00 1.11e-01 1.70e+01 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 29647 17.99 - 35.98: 3337 35.98 - 53.96: 965 53.96 - 71.95: 132 71.95 - 89.94: 79 Dihedral angle restraints: 34160 sinusoidal: 13510 harmonic: 20650 Sorted by residual: dihedral pdb=" CA GLU M 191 " pdb=" C GLU M 191 " pdb=" N GLY M 192 " pdb=" CA GLY M 192 " ideal model delta harmonic sigma weight residual 180.00 134.57 45.43 0 5.00e+00 4.00e-02 8.26e+01 dihedral pdb=" CA VAL M 190 " pdb=" C VAL M 190 " pdb=" N GLU M 191 " pdb=" CA GLU M 191 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLY M 192 " pdb=" C GLY M 192 " pdb=" N MET M 193 " pdb=" CA MET M 193 " ideal model delta harmonic sigma weight residual 180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 7211 0.050 - 0.101: 1424 0.101 - 0.151: 336 0.151 - 0.201: 1 0.201 - 0.251: 2 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CG LEU M 295 " pdb=" CB LEU M 295 " pdb=" CD1 LEU M 295 " pdb=" CD2 LEU M 295 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE B 250 " pdb=" CA ILE B 250 " pdb=" CG1 ILE B 250 " pdb=" CG2 ILE B 250 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL L 271 " pdb=" N VAL L 271 " pdb=" C VAL L 271 " pdb=" CB VAL L 271 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 234 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO L 235 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 235 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 235 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 234 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO J 235 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO J 235 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 235 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 234 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO H 235 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 235 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 235 " -0.026 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.65: 1211 2.65 - 3.27: 59936 3.27 - 3.90: 122385 3.90 - 4.52: 162493 4.52 - 5.14: 243083 Nonbonded interactions: 589108 Sorted by model distance: nonbonded pdb="MG MG G 601 " pdb=" O2A ATP G 602 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR M 90 " pdb=" O1G ATP M 602 " model vdw 2.234 2.440 nonbonded pdb="MG MG A 601 " pdb=" O2A ATP A 602 " model vdw 2.234 2.170 nonbonded pdb=" OG1 THR C 90 " pdb=" O1G ATP C 602 " model vdw 2.246 2.440 nonbonded pdb="MG MG K 601 " pdb=" O2A ATP K 602 " model vdw 2.247 2.170 ... (remaining 589103 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.460 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 112.790 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.430 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:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 0.082 54726 Z= 0.260 Angle : 0.599 14.147 73990 Z= 0.314 Chirality : 0.042 0.251 8974 Planarity : 0.004 0.060 9618 Dihedral : 16.852 89.938 20916 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.77 % Favored : 98.22 % Rotamer: Outliers : 1.77 % Allowed : 19.30 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.48 (0.09), residues: 7294 helix: 1.14 (0.08), residues: 4102 sheet: -0.33 (0.13), residues: 1218 loop : -0.83 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.030 0.001 PHE J 195 TYR 0.010 0.001 TYR M 478 ARG 0.002 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 262 time to evaluate : 4.497 Fit side-chains revert: symmetry clash REVERT: D 307 MET cc_start: 0.5834 (tpp) cc_final: 0.3584 (ttt) REVERT: E 114 MET cc_start: 0.8925 (tpp) cc_final: 0.8717 (tpp) REVERT: H 307 MET cc_start: 0.5921 (tpt) cc_final: 0.3363 (tmt) REVERT: K 114 MET cc_start: 0.8928 (tpp) cc_final: 0.8711 (tpp) REVERT: L 288 MET cc_start: 0.6082 (mmt) cc_final: 0.4943 (ptm) REVERT: L 307 MET cc_start: 0.4240 (tmm) cc_final: 0.3944 (tmm) REVERT: M 111 MET cc_start: 0.8866 (mtp) cc_final: 0.8657 (mtp) REVERT: M 288 MET cc_start: 0.5818 (ptm) cc_final: 0.5479 (ptt) outliers start: 100 outliers final: 81 residues processed: 355 average time/residue: 1.2393 time to fit residues: 572.5378 Evaluate side-chains 341 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 260 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 300 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 6.9990 chunk 551 optimal weight: 9.9990 chunk 306 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 570 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 346 optimal weight: 40.0000 chunk 424 optimal weight: 3.9990 chunk 661 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54726 Z= 0.214 Angle : 0.467 12.196 73990 Z= 0.250 Chirality : 0.040 0.157 8974 Planarity : 0.003 0.055 9618 Dihedral : 8.483 85.510 8299 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.28 % Favored : 98.71 % Rotamer: Outliers : 2.84 % Allowed : 18.34 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.82 (0.09), residues: 7294 helix: 1.46 (0.08), residues: 4116 sheet: -0.41 (0.14), residues: 1106 loop : -0.65 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.013 0.001 PHE M 44 TYR 0.008 0.001 TYR M 478 ARG 0.003 0.000 ARG I 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 261 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 307 MET cc_start: 0.6222 (tpp) cc_final: 0.5908 (tpp) REVERT: E 114 MET cc_start: 0.8931 (tpp) cc_final: 0.8711 (tpp) REVERT: H 138 CYS cc_start: 0.4055 (OUTLIER) cc_final: 0.3830 (p) REVERT: H 307 MET cc_start: 0.6025 (tpt) cc_final: 0.3004 (ttt) REVERT: H 514 MET cc_start: 0.9241 (mtp) cc_final: 0.9033 (mtm) REVERT: K 114 MET cc_start: 0.8937 (tpp) cc_final: 0.8724 (tpp) REVERT: K 213 VAL cc_start: 0.1154 (OUTLIER) cc_final: 0.0847 (m) REVERT: L 10 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8485 (t0) REVERT: L 194 GLN cc_start: 0.7593 (pm20) cc_final: 0.7374 (pm20) REVERT: L 226 LYS cc_start: 0.2092 (OUTLIER) cc_final: 0.1368 (tptt) outliers start: 160 outliers final: 70 residues processed: 401 average time/residue: 1.2758 time to fit residues: 660.3188 Evaluate side-chains 335 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 261 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 520 MET Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 226 LYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 3.9990 chunk 205 optimal weight: 0.5980 chunk 550 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 662 optimal weight: 0.0470 chunk 715 optimal weight: 0.9990 chunk 589 optimal weight: 0.7980 chunk 656 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 531 optimal weight: 0.0980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54726 Z= 0.131 Angle : 0.438 11.688 73990 Z= 0.234 Chirality : 0.039 0.156 8974 Planarity : 0.003 0.054 9618 Dihedral : 7.928 85.266 8251 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.19 % Favored : 98.79 % Rotamer: Outliers : 2.61 % Allowed : 18.79 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.10), residues: 7294 helix: 1.76 (0.08), residues: 4116 sheet: -0.13 (0.14), residues: 1218 loop : -0.74 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.016 0.001 PHE L 195 TYR 0.007 0.001 TYR B 478 ARG 0.003 0.000 ARG L 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 263 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7177 (t) REVERT: B 222 LEU cc_start: 0.1760 (OUTLIER) cc_final: 0.1426 (mp) REVERT: B 233 MET cc_start: 0.1122 (tmm) cc_final: 0.0852 (tmt) REVERT: B 365 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5811 (tp) REVERT: D 307 MET cc_start: 0.6446 (tpp) cc_final: 0.5981 (tpp) REVERT: E 114 MET cc_start: 0.8952 (tpp) cc_final: 0.8739 (tpp) REVERT: E 226 LYS cc_start: 0.1797 (OUTLIER) cc_final: 0.1111 (mmtt) REVERT: F 323 VAL cc_start: 0.6730 (OUTLIER) cc_final: 0.6443 (t) REVERT: H 307 MET cc_start: 0.6109 (tpt) cc_final: 0.3343 (ttp) REVERT: H 514 MET cc_start: 0.9248 (mtp) cc_final: 0.9001 (mtm) REVERT: I 514 MET cc_start: 0.9285 (mtp) cc_final: 0.9041 (mtm) REVERT: J 193 MET cc_start: 0.6609 (mmm) cc_final: 0.6409 (mmm) REVERT: M 193 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6695 (mmp) outliers start: 147 outliers final: 67 residues processed: 389 average time/residue: 1.2469 time to fit residues: 630.1444 Evaluate side-chains 335 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 262 time to evaluate : 5.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 0.5980 chunk 497 optimal weight: 40.0000 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 316 optimal weight: 1.9990 chunk 444 optimal weight: 5.9990 chunk 664 optimal weight: 0.0670 chunk 703 optimal weight: 8.9990 chunk 347 optimal weight: 0.9980 chunk 629 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54726 Z= 0.262 Angle : 0.476 12.972 73990 Z= 0.253 Chirality : 0.040 0.159 8974 Planarity : 0.003 0.055 9618 Dihedral : 7.996 86.914 8240 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.40 % Favored : 98.59 % Rotamer: Outliers : 2.80 % Allowed : 19.02 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.10), residues: 7294 helix: 1.69 (0.08), residues: 4102 sheet: -0.15 (0.14), residues: 1218 loop : -0.79 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.014 0.001 PHE A 44 TYR 0.009 0.001 TYR M 478 ARG 0.003 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 260 time to evaluate : 4.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7197 (t) REVERT: B 222 LEU cc_start: 0.1852 (OUTLIER) cc_final: 0.1492 (mp) REVERT: B 233 MET cc_start: 0.1433 (tmm) cc_final: 0.1167 (tmm) REVERT: B 365 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5961 (tp) REVERT: D 307 MET cc_start: 0.6497 (tpp) cc_final: 0.6019 (tpp) REVERT: E 114 MET cc_start: 0.8940 (tpp) cc_final: 0.8724 (tpp) REVERT: E 226 LYS cc_start: 0.1900 (OUTLIER) cc_final: 0.1288 (mmtt) REVERT: E 323 VAL cc_start: 0.7288 (OUTLIER) cc_final: 0.6979 (t) REVERT: F 323 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6529 (t) REVERT: H 138 CYS cc_start: 0.4193 (OUTLIER) cc_final: 0.3934 (p) REVERT: H 484 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7874 (pp20) REVERT: H 514 MET cc_start: 0.9242 (mtp) cc_final: 0.8991 (mtm) REVERT: I 514 MET cc_start: 0.9281 (mtp) cc_final: 0.9073 (mtm) REVERT: J 193 MET cc_start: 0.6732 (mmm) cc_final: 0.6423 (mmm) REVERT: K 111 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8671 (mtp) REVERT: L 10 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8492 (t0) REVERT: M 193 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6710 (mmp) REVERT: N 307 MET cc_start: 0.4585 (tmm) cc_final: 0.4138 (tmm) outliers start: 158 outliers final: 93 residues processed: 403 average time/residue: 1.2165 time to fit residues: 639.6993 Evaluate side-chains 363 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 259 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 3.9990 chunk 399 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 523 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 chunk 600 optimal weight: 7.9990 chunk 486 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 631 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54726 Z= 0.182 Angle : 0.458 12.656 73990 Z= 0.243 Chirality : 0.039 0.152 8974 Planarity : 0.003 0.054 9618 Dihedral : 7.848 86.128 8237 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.22 % Favored : 98.77 % Rotamer: Outliers : 2.80 % Allowed : 19.16 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.10), residues: 7294 helix: 1.76 (0.08), residues: 4102 sheet: -0.11 (0.14), residues: 1218 loop : -0.76 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.015 0.001 PHE B 44 TYR 0.008 0.001 TYR G 478 ARG 0.002 0.000 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 261 time to evaluate : 5.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7205 (t) REVERT: B 222 LEU cc_start: 0.1564 (OUTLIER) cc_final: 0.1230 (mp) REVERT: B 233 MET cc_start: 0.1422 (tmm) cc_final: 0.1147 (tmm) REVERT: B 365 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5798 (tp) REVERT: C 233 MET cc_start: -0.0023 (tmm) cc_final: -0.0268 (tmt) REVERT: D 307 MET cc_start: 0.6542 (tpp) cc_final: 0.6091 (tpp) REVERT: E 114 MET cc_start: 0.8942 (tpp) cc_final: 0.8731 (tpp) REVERT: E 226 LYS cc_start: 0.1793 (OUTLIER) cc_final: 0.1185 (mmtt) REVERT: E 323 VAL cc_start: 0.7289 (OUTLIER) cc_final: 0.6984 (t) REVERT: F 140 ASP cc_start: 0.4475 (OUTLIER) cc_final: 0.3283 (p0) REVERT: F 323 VAL cc_start: 0.6845 (OUTLIER) cc_final: 0.6563 (t) REVERT: H 111 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8075 (mmp) REVERT: H 138 CYS cc_start: 0.4164 (OUTLIER) cc_final: 0.3932 (p) REVERT: H 307 MET cc_start: 0.5899 (tpt) cc_final: 0.3088 (ttp) REVERT: H 484 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7857 (pp20) REVERT: I 140 ASP cc_start: 0.4553 (OUTLIER) cc_final: 0.3428 (p0) REVERT: I 288 MET cc_start: 0.6394 (ptm) cc_final: 0.6189 (ptt) REVERT: I 514 MET cc_start: 0.9290 (mtp) cc_final: 0.9019 (mtm) REVERT: J 193 MET cc_start: 0.6626 (mmm) cc_final: 0.6260 (mmm) REVERT: K 111 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8723 (mtp) REVERT: L 10 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8499 (t0) REVERT: M 193 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6771 (mmp) outliers start: 158 outliers final: 96 residues processed: 404 average time/residue: 1.2147 time to fit residues: 645.2732 Evaluate side-chains 369 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 259 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 502 SER Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 40.0000 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 704 optimal weight: 10.0000 chunk 584 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 40.0000 chunk 369 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN I 37 ASN ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54726 Z= 0.247 Angle : 0.485 12.317 73990 Z= 0.255 Chirality : 0.040 0.147 8974 Planarity : 0.003 0.055 9618 Dihedral : 7.951 86.443 8233 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.44 % Favored : 98.55 % Rotamer: Outliers : 2.64 % Allowed : 19.60 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7294 helix: 1.68 (0.08), residues: 4102 sheet: -0.28 (0.14), residues: 1106 loop : -0.62 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.015 0.001 PHE A 44 TYR 0.009 0.001 TYR M 478 ARG 0.002 0.000 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 261 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7232 (t) REVERT: B 222 LEU cc_start: 0.1645 (OUTLIER) cc_final: 0.1275 (mp) REVERT: B 233 MET cc_start: 0.1270 (tmm) cc_final: 0.0978 (tmm) REVERT: B 365 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6056 (tp) REVERT: D 307 MET cc_start: 0.6728 (tpp) cc_final: 0.6291 (tpp) REVERT: E 111 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8575 (mtp) REVERT: E 114 MET cc_start: 0.8941 (tpp) cc_final: 0.8725 (tpp) REVERT: E 226 LYS cc_start: 0.1833 (OUTLIER) cc_final: 0.1232 (mmtt) REVERT: E 323 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.7038 (t) REVERT: F 140 ASP cc_start: 0.4750 (OUTLIER) cc_final: 0.3549 (p0) REVERT: F 323 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6720 (t) REVERT: H 111 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8072 (mmp) REVERT: H 138 CYS cc_start: 0.4283 (OUTLIER) cc_final: 0.4027 (p) REVERT: H 307 MET cc_start: 0.5972 (tpt) cc_final: 0.3232 (ttp) REVERT: H 484 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: I 140 ASP cc_start: 0.4566 (OUTLIER) cc_final: 0.3398 (p0) REVERT: I 307 MET cc_start: 0.4582 (tmm) cc_final: 0.4357 (tpt) REVERT: I 514 MET cc_start: 0.9307 (mtp) cc_final: 0.9023 (mtm) REVERT: K 111 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8660 (mtp) REVERT: L 10 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8503 (t0) REVERT: M 193 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6763 (mmp) REVERT: M 233 MET cc_start: -0.0148 (tmm) cc_final: -0.0398 (tmt) REVERT: N 307 MET cc_start: 0.4658 (tmm) cc_final: 0.4233 (tmm) outliers start: 149 outliers final: 95 residues processed: 393 average time/residue: 1.1862 time to fit residues: 610.2379 Evaluate side-chains 370 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 260 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 401 optimal weight: 10.0000 chunk 514 optimal weight: 0.9980 chunk 398 optimal weight: 7.9990 chunk 592 optimal weight: 4.9990 chunk 393 optimal weight: 7.9990 chunk 701 optimal weight: 0.9990 chunk 439 optimal weight: 20.0000 chunk 427 optimal weight: 0.7980 chunk 323 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 ASN N 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54726 Z= 0.202 Angle : 0.474 12.198 73990 Z= 0.249 Chirality : 0.039 0.146 8974 Planarity : 0.003 0.054 9618 Dihedral : 7.820 86.298 8232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.32 % Favored : 98.67 % Rotamer: Outliers : 2.61 % Allowed : 19.78 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.10), residues: 7294 helix: 1.74 (0.08), residues: 4102 sheet: -0.26 (0.14), residues: 1106 loop : -0.59 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.015 0.001 PHE B 44 TYR 0.008 0.001 TYR M 478 ARG 0.009 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 261 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7266 (p) REVERT: B 222 LEU cc_start: 0.1629 (OUTLIER) cc_final: 0.1228 (mp) REVERT: B 233 MET cc_start: 0.1161 (tmm) cc_final: 0.0945 (tmm) REVERT: B 365 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6250 (tp) REVERT: D 307 MET cc_start: 0.6738 (tpp) cc_final: 0.6313 (tpp) REVERT: E 111 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8605 (mtp) REVERT: E 114 MET cc_start: 0.8942 (tpp) cc_final: 0.8731 (tpp) REVERT: E 226 LYS cc_start: 0.1788 (OUTLIER) cc_final: 0.1183 (mmtt) REVERT: E 323 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7043 (t) REVERT: F 140 ASP cc_start: 0.4754 (OUTLIER) cc_final: 0.3555 (p0) REVERT: F 323 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6756 (t) REVERT: H 111 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8070 (mmp) REVERT: H 138 CYS cc_start: 0.4265 (OUTLIER) cc_final: 0.4024 (p) REVERT: H 226 LYS cc_start: 0.1922 (OUTLIER) cc_final: 0.1444 (mptp) REVERT: H 307 MET cc_start: 0.5931 (tpt) cc_final: 0.3185 (ttp) REVERT: H 484 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7852 (pp20) REVERT: H 514 MET cc_start: 0.9256 (mtp) cc_final: 0.9046 (mtm) REVERT: I 75 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8513 (ttpt) REVERT: I 140 ASP cc_start: 0.4508 (OUTLIER) cc_final: 0.3342 (p0) REVERT: I 514 MET cc_start: 0.9292 (mtp) cc_final: 0.9013 (mtm) REVERT: J 193 MET cc_start: 0.6573 (mmm) cc_final: 0.6270 (mmm) REVERT: K 111 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8674 (mtp) REVERT: L 10 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8524 (t0) REVERT: M 233 MET cc_start: -0.0294 (tmm) cc_final: -0.0544 (tmt) REVERT: N 307 MET cc_start: 0.4753 (tmm) cc_final: 0.4353 (tmm) outliers start: 147 outliers final: 103 residues processed: 395 average time/residue: 1.2088 time to fit residues: 623.7110 Evaluate side-chains 378 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 259 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 226 LYS Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 419 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 446 optimal weight: 30.0000 chunk 478 optimal weight: 0.7980 chunk 346 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 551 optimal weight: 40.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 ASN J 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 54726 Z= 0.307 Angle : 0.520 12.279 73990 Z= 0.271 Chirality : 0.041 0.142 8974 Planarity : 0.003 0.053 9618 Dihedral : 8.077 88.328 8231 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.56 % Favored : 98.42 % Rotamer: Outliers : 2.68 % Allowed : 19.99 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.94 (0.09), residues: 7294 helix: 1.56 (0.08), residues: 4102 sheet: -0.29 (0.14), residues: 1106 loop : -0.65 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.016 0.001 PHE A 44 TYR 0.011 0.001 TYR C 478 ARG 0.006 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 263 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 LEU cc_start: 0.1692 (OUTLIER) cc_final: 0.1279 (mp) REVERT: B 233 MET cc_start: 0.1182 (tmm) cc_final: 0.0966 (tmm) REVERT: C 140 ASP cc_start: 0.4688 (OUTLIER) cc_final: 0.4088 (p0) REVERT: D 307 MET cc_start: 0.6848 (tpp) cc_final: 0.6377 (tpp) REVERT: E 114 MET cc_start: 0.8914 (tpp) cc_final: 0.8703 (tpp) REVERT: E 226 LYS cc_start: 0.1762 (OUTLIER) cc_final: 0.1140 (mttt) REVERT: E 323 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7123 (t) REVERT: F 140 ASP cc_start: 0.4790 (OUTLIER) cc_final: 0.3546 (p0) REVERT: F 323 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6816 (t) REVERT: H 111 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8076 (mmp) REVERT: H 138 CYS cc_start: 0.4398 (OUTLIER) cc_final: 0.4141 (p) REVERT: H 226 LYS cc_start: 0.1941 (OUTLIER) cc_final: 0.1463 (mptp) REVERT: H 307 MET cc_start: 0.6139 (tpt) cc_final: 0.3436 (ttp) REVERT: H 447 MET cc_start: 0.9160 (mtp) cc_final: 0.8951 (mtm) REVERT: H 484 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7874 (pp20) REVERT: H 514 MET cc_start: 0.9281 (mtp) cc_final: 0.9032 (mtm) REVERT: I 140 ASP cc_start: 0.4523 (OUTLIER) cc_final: 0.3251 (p0) REVERT: I 288 MET cc_start: 0.6439 (ptm) cc_final: 0.6217 (ptt) REVERT: I 307 MET cc_start: 0.4949 (tmm) cc_final: 0.4674 (tpt) REVERT: I 514 MET cc_start: 0.9314 (mtp) cc_final: 0.9034 (mtm) REVERT: J 140 ASP cc_start: 0.4545 (OUTLIER) cc_final: 0.3237 (p0) REVERT: J 193 MET cc_start: 0.6473 (mmm) cc_final: 0.6129 (mmm) REVERT: J 263 VAL cc_start: 0.1546 (OUTLIER) cc_final: 0.1180 (t) REVERT: K 111 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8611 (mtp) REVERT: N 307 MET cc_start: 0.4781 (tmm) cc_final: 0.4354 (tmm) outliers start: 151 outliers final: 102 residues processed: 400 average time/residue: 1.1812 time to fit residues: 619.5362 Evaluate side-chains 380 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 264 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 226 LYS Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 4.9990 chunk 672 optimal weight: 0.9990 chunk 613 optimal weight: 6.9990 chunk 653 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 513 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 590 optimal weight: 4.9990 chunk 618 optimal weight: 2.9990 chunk 651 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54726 Z= 0.285 Angle : 0.519 12.624 73990 Z= 0.270 Chirality : 0.041 0.157 8974 Planarity : 0.003 0.052 9618 Dihedral : 7.986 87.150 8228 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.43 % Favored : 98.56 % Rotamer: Outliers : 2.45 % Allowed : 20.38 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.92 (0.09), residues: 7294 helix: 1.55 (0.08), residues: 4102 sheet: -0.30 (0.14), residues: 1106 loop : -0.65 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.014 0.001 PHE M 44 TYR 0.011 0.001 TYR M 478 ARG 0.005 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 270 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 233 MET cc_start: 0.1115 (tmm) cc_final: 0.0905 (tmm) REVERT: D 307 MET cc_start: 0.6864 (tpp) cc_final: 0.6388 (tpp) REVERT: E 111 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: E 114 MET cc_start: 0.8917 (tpp) cc_final: 0.8698 (tpp) REVERT: E 226 LYS cc_start: 0.1803 (OUTLIER) cc_final: 0.1170 (mttt) REVERT: E 323 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7170 (t) REVERT: F 140 ASP cc_start: 0.4590 (OUTLIER) cc_final: 0.3372 (p0) REVERT: F 323 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6877 (t) REVERT: H 111 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8095 (mmp) REVERT: H 226 LYS cc_start: 0.1928 (OUTLIER) cc_final: 0.1437 (mptp) REVERT: H 307 MET cc_start: 0.6239 (tpt) cc_final: 0.3579 (ttp) REVERT: H 447 MET cc_start: 0.9155 (mtp) cc_final: 0.8948 (mtm) REVERT: H 484 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: H 514 MET cc_start: 0.9290 (mtp) cc_final: 0.9046 (mtm) REVERT: I 140 ASP cc_start: 0.4478 (OUTLIER) cc_final: 0.3224 (p0) REVERT: I 514 MET cc_start: 0.9310 (mtp) cc_final: 0.9033 (mtm) REVERT: J 140 ASP cc_start: 0.4565 (OUTLIER) cc_final: 0.3164 (p0) REVERT: J 193 MET cc_start: 0.6528 (mmm) cc_final: 0.6185 (mmm) REVERT: J 263 VAL cc_start: 0.1548 (OUTLIER) cc_final: 0.1172 (t) REVERT: K 111 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8645 (mtp) REVERT: N 307 MET cc_start: 0.4852 (tmm) cc_final: 0.4432 (tmm) outliers start: 138 outliers final: 105 residues processed: 395 average time/residue: 1.2049 time to fit residues: 622.2021 Evaluate side-chains 382 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 264 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 226 LYS Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 2.9990 chunk 691 optimal weight: 0.9980 chunk 422 optimal weight: 0.8980 chunk 328 optimal weight: 9.9990 chunk 480 optimal weight: 0.7980 chunk 725 optimal weight: 1.9990 chunk 667 optimal weight: 0.9990 chunk 577 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 446 optimal weight: 0.0570 chunk 354 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54726 Z= 0.152 Angle : 0.485 13.026 73990 Z= 0.252 Chirality : 0.039 0.135 8974 Planarity : 0.003 0.053 9618 Dihedral : 7.654 85.715 8226 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.28 % Favored : 98.71 % Rotamer: Outliers : 1.93 % Allowed : 20.91 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.10), residues: 7294 helix: 1.79 (0.08), residues: 4102 sheet: -0.08 (0.14), residues: 1218 loop : -0.74 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS M 401 PHE 0.016 0.001 PHE A 44 TYR 0.009 0.001 TYR M 478 ARG 0.005 0.000 ARG D 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 270 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7407 (p) REVERT: B 233 MET cc_start: 0.1073 (tmm) cc_final: 0.0863 (tmm) REVERT: C 140 ASP cc_start: 0.4610 (OUTLIER) cc_final: 0.4026 (p0) REVERT: D 307 MET cc_start: 0.6806 (tpp) cc_final: 0.6340 (tpp) REVERT: E 111 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8663 (mtp) REVERT: E 114 MET cc_start: 0.8946 (tpp) cc_final: 0.8734 (tpp) REVERT: E 193 MET cc_start: 0.6140 (mmm) cc_final: 0.5616 (mmm) REVERT: E 226 LYS cc_start: 0.1780 (OUTLIER) cc_final: 0.1156 (mttt) REVERT: F 140 ASP cc_start: 0.4590 (OUTLIER) cc_final: 0.3406 (p0) REVERT: F 323 VAL cc_start: 0.7145 (OUTLIER) cc_final: 0.6854 (t) REVERT: H 226 LYS cc_start: 0.1925 (OUTLIER) cc_final: 0.1402 (mptp) REVERT: H 307 MET cc_start: 0.6201 (tpt) cc_final: 0.3542 (ttp) REVERT: H 484 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7845 (pp20) REVERT: H 514 MET cc_start: 0.9272 (mtp) cc_final: 0.9019 (mtm) REVERT: I 75 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8639 (ttpt) REVERT: I 514 MET cc_start: 0.9274 (mtp) cc_final: 0.8994 (mtm) REVERT: J 140 ASP cc_start: 0.4427 (OUTLIER) cc_final: 0.3145 (p0) REVERT: J 193 MET cc_start: 0.6471 (mmm) cc_final: 0.6158 (mmm) REVERT: J 263 VAL cc_start: 0.1519 (OUTLIER) cc_final: 0.1147 (t) REVERT: K 111 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: K 233 MET cc_start: 0.0924 (tmm) cc_final: 0.0679 (tmm) REVERT: M 288 MET cc_start: 0.5771 (ptm) cc_final: 0.5475 (ptt) outliers start: 109 outliers final: 85 residues processed: 375 average time/residue: 1.2427 time to fit residues: 604.7159 Evaluate side-chains 363 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 266 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 226 LYS Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 0.3980 chunk 615 optimal weight: 3.9990 chunk 176 optimal weight: 0.0980 chunk 532 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 0.0980 chunk 578 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 593 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.167209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104332 restraints weight = 79110.503| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.77 r_work: 0.3110 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 54726 Z= 0.138 Angle : 0.478 12.452 73990 Z= 0.248 Chirality : 0.039 0.135 8974 Planarity : 0.003 0.054 9618 Dihedral : 7.427 87.116 8219 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.17 % Favored : 98.82 % Rotamer: Outliers : 1.67 % Allowed : 21.45 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 7294 helix: 1.92 (0.08), residues: 4102 sheet: -0.02 (0.14), residues: 1218 loop : -0.71 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS M 401 PHE 0.023 0.001 PHE J 195 TYR 0.008 0.001 TYR B 478 ARG 0.004 0.000 ARG D 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12521.13 seconds wall clock time: 222 minutes 41.03 seconds (13361.03 seconds total)