Starting phenix.real_space_refine on Mon Mar 11 06:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blc_16106/03_2024/8blc_16106_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blc_16106/03_2024/8blc_16106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blc_16106/03_2024/8blc_16106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blc_16106/03_2024/8blc_16106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blc_16106/03_2024/8blc_16106_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blc_16106/03_2024/8blc_16106_updated.pdb" } resolution = 2.7 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 12288 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 238": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F ASP 359": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 304": "OE1" <-> "OE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J ASP 83": "OD1" <-> "OD2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 257": "OE1" <-> "OE2" Residue "M ASP 359": "OD1" <-> "OD2" Residue "M GLU 483": "OE1" <-> "OE2" Residue "N GLU 63": "OE1" <-> "OE2" Residue "N ASP 224": "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: 55646 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: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "F" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "H" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "J" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "L" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} 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: 21.45, per 1000 atoms: 0.39 Number of scatterers: 55646 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 12288 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: 18.41 Conformation dependent library (CDL) restraints added in 7.5 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: 279 helices and 101 sheets defined 52.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.50 Creating SS restraints... Processing helix chain 'G' and resid 9 through 30 removed outlier: 4.846A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 removed outlier: 3.535A pdb=" N GLU G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.874A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.676A 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 266 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 374 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 457 removed outlier: 3.817A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.903A 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: 3.808A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 30 removed outlier: 4.735A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.540A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.864A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.676A 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 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 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' 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 457 removed outlier: 3.818A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.903A 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: 3.802A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 removed outlier: 4.856A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.932A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.670A 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 169 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 234 through 242 Processing helix chain 'B' and resid 260 through 266 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' 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 425 Processing helix chain 'B' and resid 434 through 457 removed outlier: 3.775A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.821A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 30 removed outlier: 4.882A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 65 through 84 removed outlier: 4.022A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.820A 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 169 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: 3.835A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.902A 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: 3.742A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 removed outlier: 4.749A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.868A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.570A 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 169 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: 3.823A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.905A 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: 3.788A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 30 removed outlier: 4.720A 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 84 removed outlier: 3.984A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.688A 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 169 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 457 removed outlier: 3.792A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.758A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 removed outlier: 4.722A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 58 Processing helix chain 'F' and resid 65 through 84 removed outlier: 3.882A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.600A 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 168 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 457 removed outlier: 3.826A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.917A 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: 3.769A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 30 removed outlier: 4.780A 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: 3.902A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.673A 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 169 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 231 through 242 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: 3.786A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.816A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 30 removed outlier: 4.750A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.908A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.676A 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 169 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 241 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 374 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: 3.795A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.820A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 30 removed outlier: 4.729A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 Processing helix chain 'J' and resid 65 through 84 removed outlier: 3.903A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.616A 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 457 removed outlier: 3.811A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.904A 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: 3.754A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 30 removed outlier: 4.719A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 58 Processing helix chain 'K' and resid 65 through 84 removed outlier: 3.982A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.675A 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 169 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 260 through 266 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 425 Processing helix chain 'K' and resid 434 through 457 removed outlier: 3.793A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.750A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 4.747A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 58 Processing helix chain 'L' and resid 65 through 85 removed outlier: 3.995A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.821A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.906A 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: 3.794A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 30 removed outlier: 4.848A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.566A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.983A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.653A 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 169 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 260 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: 3.828A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 3.906A 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: 3.732A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 30 removed outlier: 4.846A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 58 Processing helix chain 'N' and resid 65 through 84 removed outlier: 3.841A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.688A 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 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 231 through 242 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 309 through 311 No H-bonds generated for 'chain 'N' and resid 309 through 311' 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 425 Processing helix chain 'N' and resid 434 through 457 removed outlier: 3.768A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.899A 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: 3.821A 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 219 through 222 Processing sheet with id= F, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= K, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= L, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= M, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= P, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= Q, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= R, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= S, first strand: chain 'B' and resid 213 through 216 Processing sheet with id= T, first strand: chain 'B' and resid 219 through 221 Processing sheet with id= U, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= V, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= W, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= X, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= Y, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= Z, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AA, first strand: chain 'C' and resid 219 through 222 removed outlier: 7.054A pdb=" N ALA C 274 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AC, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= AD, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AE, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AF, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AG, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AH, first strand: chain 'D' and resid 213 through 216 Processing sheet with id= AI, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AJ, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AK, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AL, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AM, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AN, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AO, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AP, first strand: chain 'E' and resid 219 through 222 removed outlier: 6.951A pdb=" N ALA E 274 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AR, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AS, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AT, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AU, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AV, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= AW, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AX, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AY, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AZ, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= BA, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= BB, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= BC, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= BD, first strand: chain 'H' and resid 219 through 222 removed outlier: 6.822A pdb=" N ALA H 274 " --> pdb=" O ILE H 249 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BF, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BG, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BH, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BI, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BJ, first strand: chain 'I' and resid 193 through 195 Processing sheet with id= BK, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BL, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BM, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BN, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BO, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BP, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BQ, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= BR, first strand: chain 'J' and resid 219 through 222 removed outlier: 6.777A pdb=" N ALA J 274 " --> pdb=" O ILE J 249 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BT, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BU, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= BX, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= BY, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.893A pdb=" N ALA K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= CA, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= CB, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CC, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CD, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CE, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CF, first strand: chain 'L' and resid 219 through 222 removed outlier: 6.808A pdb=" N ALA L 274 " --> pdb=" O ILE L 249 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CH, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CI, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CJ, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CK, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CL, first strand: chain 'M' and resid 193 through 195 removed outlier: 4.220A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'M' and resid 213 through 216 Processing sheet with id= CN, first strand: chain 'M' and resid 219 through 222 removed outlier: 6.846A pdb=" N ALA M 274 " --> pdb=" O ILE M 249 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CP, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CQ, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= CR, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CS, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= CT, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= CU, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= CV, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= CW, first strand: chain 'N' and resid 476 through 479 3141 hydrogen bonds defined for protein. 9072 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: 22.19 Time building geometry restraints manager: 20.06 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: 18830 1.34 - 1.46: 9645 1.46 - 1.58: 25719 1.58 - 1.70: 14 1.70 - 1.82: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" SD MET F 69 " pdb=" CE MET F 69 " ideal model delta sigma weight residual 1.791 1.735 0.056 2.50e-02 1.60e+03 5.06e+00 bond pdb=" SD MET J 69 " pdb=" CE MET J 69 " ideal model delta sigma weight residual 1.791 1.749 0.042 2.50e-02 1.60e+03 2.78e+00 bond pdb=" CG1 ILE A 353 " pdb=" CD1 ILE A 353 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.55e+00 bond pdb=" CG LEU G 31 " pdb=" CD2 LEU G 31 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" O3A ATP M 602 " pdb=" PA ATP M 602 " ideal model delta sigma weight residual 1.592 1.555 0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 96.93 - 105.55: 892 105.55 - 114.16: 33715 114.16 - 122.78: 34904 122.78 - 131.39: 4437 131.39 - 140.00: 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 113.18 124.55 -11.37 2.37e+00 1.78e-01 2.30e+01 angle pdb=" CA MET C 233 " pdb=" CB MET C 233 " pdb=" CG MET C 233 " ideal model delta sigma weight residual 114.10 123.59 -9.49 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CA MET I 233 " pdb=" CB MET I 233 " pdb=" CG MET I 233 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB MET D 193 " pdb=" CG MET D 193 " pdb=" SD MET D 193 " ideal model delta sigma weight residual 112.70 123.52 -10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET C 233 " pdb=" CG MET C 233 " pdb=" SD MET C 233 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.20e+01 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 29666 17.84 - 35.68: 3218 35.68 - 53.53: 1039 53.53 - 71.37: 139 71.37 - 89.21: 98 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 180.00 146.93 33.07 0 5.00e+00 4.00e-02 4.37e+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 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+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 -161.46 -18.54 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 7996 0.066 - 0.132: 957 0.132 - 0.198: 20 0.198 - 0.263: 0 0.263 - 0.329: 1 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CB ILE A 353 " pdb=" CA ILE A 353 " pdb=" CG1 ILE A 353 " pdb=" CG2 ILE A 353 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA PRO A 462 " pdb=" N PRO A 462 " pdb=" C PRO A 462 " pdb=" CB PRO A 462 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO C 462 " pdb=" N PRO C 462 " pdb=" C PRO C 462 " pdb=" CB PRO C 462 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 233 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C MET C 233 " 0.029 2.00e-02 2.50e+03 pdb=" O MET C 233 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 234 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 362 " 0.139 9.50e-02 1.11e+02 6.22e-02 2.54e+00 pdb=" NE ARG A 362 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 362 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 362 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 362 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 233 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C MET I 233 " -0.026 2.00e-02 2.50e+03 pdb=" O MET I 233 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU I 234 " 0.009 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.68: 1613 2.68 - 3.29: 64263 3.29 - 3.91: 124498 3.91 - 4.52: 165656 4.52 - 5.14: 242790 Nonbonded interactions: 598820 Sorted by model distance: nonbonded pdb=" OD1 ASP I 87 " pdb="MG MG I 601 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP H 87 " pdb="MG MG H 601 " model vdw 2.065 2.170 nonbonded pdb=" OD1 ASP D 87 " pdb="MG MG D 601 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP L 87 " pdb="MG MG L 601 " model vdw 2.089 2.170 nonbonded pdb=" OD1 ASP A 87 " pdb="MG MG A 601 " model vdw 2.097 2.170 ... (remaining 598815 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: 0.010 Normalize map: mean=0, sd=1: 2.690 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: 13.400 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 120.550 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.470 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:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.005 0.062 54726 Z= 0.305 Angle : 0.514 11.375 73990 Z= 0.278 Chirality : 0.042 0.329 8974 Planarity : 0.003 0.062 9618 Dihedral : 17.029 89.212 20916 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.89 % Favored : 99.10 % Rotamer: Outliers : 1.44 % Allowed : 19.41 % Favored : 79.16 % 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: 1.56 (0.08), residues: 4130 sheet: 0.61 (0.15), residues: 826 loop : -0.61 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 401 PHE 0.021 0.002 PHE G 44 TYR 0.011 0.001 TYR K 506 ARG 0.007 0.000 ARG A 362 *********************** 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 372 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 291 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1826 (pp-130) cc_final: 0.0643 (tmt) REVERT: C 233 MET cc_start: 0.5514 (tmt) cc_final: 0.4890 (pp-130) REVERT: D 185 ASP cc_start: 0.7924 (m-30) cc_final: 0.7550 (m-30) REVERT: E 288 MET cc_start: 0.6130 (mmm) cc_final: 0.4751 (pp-130) REVERT: F 193 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4809 (tmt) REVERT: I 233 MET cc_start: 0.5376 (tmt) cc_final: 0.4290 (pp-130) REVERT: I 288 MET cc_start: 0.5680 (mmp) cc_final: 0.4185 (pp-130) REVERT: L 185 ASP cc_start: 0.7836 (m-30) cc_final: 0.7480 (m-30) outliers start: 81 outliers final: 61 residues processed: 370 average time/residue: 1.2871 time to fit residues: 616.6259 Evaluate side-chains 354 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 292 time to evaluate : 4.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 502 SER Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain N residue 502 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 2.9990 chunk 551 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 188 optimal weight: 20.0000 chunk 372 optimal weight: 0.9980 chunk 294 optimal weight: 8.9990 chunk 570 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 346 optimal weight: 50.0000 chunk 424 optimal weight: 0.9990 chunk 661 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN H 366 GLN J 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 54726 Z= 0.210 Angle : 0.446 11.103 73990 Z= 0.243 Chirality : 0.040 0.135 8974 Planarity : 0.003 0.051 9618 Dihedral : 8.102 78.692 8274 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.89 % Favored : 99.10 % Rotamer: Outliers : 2.07 % Allowed : 18.68 % Favored : 79.24 % 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: 1.25 (0.10), residues: 7294 helix: 1.62 (0.08), residues: 4144 sheet: 0.22 (0.14), residues: 1176 loop : -0.37 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS N 401 PHE 0.011 0.001 PHE J 44 TYR 0.008 0.001 TYR K 506 ARG 0.007 0.000 ARG E 362 *********************** 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 413 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 296 time to evaluate : 4.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1802 (pp-130) cc_final: 0.0739 (tmt) REVERT: A 234 LEU cc_start: 0.3268 (OUTLIER) cc_final: 0.3053 (tm) REVERT: C 233 MET cc_start: 0.5301 (tmt) cc_final: 0.4761 (pmt) REVERT: D 185 ASP cc_start: 0.7921 (m-30) cc_final: 0.7537 (m-30) REVERT: D 193 MET cc_start: 0.5113 (tpt) cc_final: 0.4354 (tmt) REVERT: E 233 MET cc_start: 0.6402 (tmt) cc_final: 0.5959 (pp-130) REVERT: E 267 MET cc_start: 0.1455 (OUTLIER) cc_final: 0.0799 (pp-130) REVERT: E 288 MET cc_start: 0.6281 (mmm) cc_final: 0.5064 (ppp) REVERT: I 233 MET cc_start: 0.5126 (tmt) cc_final: 0.4291 (pp-130) REVERT: K 76 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: L 233 MET cc_start: 0.1560 (OUTLIER) cc_final: 0.0309 (pmt) REVERT: N 111 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8021 (mtp) outliers start: 117 outliers final: 23 residues processed: 393 average time/residue: 1.3384 time to fit residues: 673.1732 Evaluate side-chains 318 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 550 optimal weight: 50.0000 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 662 optimal weight: 8.9990 chunk 715 optimal weight: 2.9990 chunk 589 optimal weight: 1.9990 chunk 656 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 531 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN C 37 ASN E 37 ASN H 37 ASN H 366 GLN J 366 GLN K 37 ASN K 366 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 54726 Z= 0.368 Angle : 0.507 10.806 73990 Z= 0.275 Chirality : 0.043 0.174 8974 Planarity : 0.003 0.049 9618 Dihedral : 8.488 84.095 8211 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.88 % Favored : 99.11 % Rotamer: Outliers : 2.09 % Allowed : 18.79 % Favored : 79.12 % 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: 0.97 (0.09), residues: 7294 helix: 1.43 (0.08), residues: 4130 sheet: 0.51 (0.15), residues: 826 loop : -0.65 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 401 PHE 0.014 0.001 PHE E 44 TYR 0.013 0.002 TYR C 506 ARG 0.009 0.000 ARG E 362 *********************** 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: 118 poor density : 292 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1672 (pp-130) cc_final: 0.0989 (tmt) REVERT: A 234 LEU cc_start: 0.3219 (OUTLIER) cc_final: 0.3000 (tm) REVERT: A 267 MET cc_start: 0.1755 (OUTLIER) cc_final: 0.1019 (pp-130) REVERT: C 233 MET cc_start: 0.5402 (tmt) cc_final: 0.4924 (pmt) REVERT: C 267 MET cc_start: -0.0247 (mtt) cc_final: -0.2217 (ppp) REVERT: D 185 ASP cc_start: 0.7941 (m-30) cc_final: 0.7609 (m-30) REVERT: D 307 MET cc_start: 0.2084 (tmt) cc_final: 0.1875 (tpt) REVERT: E 233 MET cc_start: 0.6381 (tmt) cc_final: 0.5927 (pmt) REVERT: E 267 MET cc_start: 0.1470 (OUTLIER) cc_final: 0.0765 (pp-130) REVERT: F 193 MET cc_start: 0.5183 (tpt) cc_final: 0.4950 (tmt) REVERT: F 267 MET cc_start: 0.0953 (OUTLIER) cc_final: 0.0269 (pp-130) REVERT: F 288 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.4893 (ppp) REVERT: H 288 MET cc_start: 0.5699 (mmp) cc_final: 0.4365 (pp-130) REVERT: I 114 MET cc_start: 0.9194 (tpp) cc_final: 0.8940 (tpt) REVERT: I 233 MET cc_start: 0.4905 (tmt) cc_final: 0.4675 (pp-130) REVERT: K 76 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: L 233 MET cc_start: 0.1574 (OUTLIER) cc_final: 0.0317 (pmt) REVERT: N 73 MET cc_start: 0.8893 (mtm) cc_final: 0.8671 (mtm) REVERT: N 111 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7987 (mtt) REVERT: N 272 LYS cc_start: 0.3519 (OUTLIER) cc_final: 0.1688 (mttm) outliers start: 118 outliers final: 44 residues processed: 388 average time/residue: 1.2564 time to fit residues: 631.7211 Evaluate side-chains 344 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 291 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 75 LYS Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 272 LYS Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 40.0000 chunk 497 optimal weight: 10.0000 chunk 343 optimal weight: 0.2980 chunk 73 optimal weight: 40.0000 chunk 316 optimal weight: 0.7980 chunk 444 optimal weight: 7.9990 chunk 664 optimal weight: 0.9990 chunk 703 optimal weight: 9.9990 chunk 347 optimal weight: 50.0000 chunk 629 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN K 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0477 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= 0.299 Angle : 0.479 11.045 73990 Z= 0.261 Chirality : 0.041 0.172 8974 Planarity : 0.003 0.050 9618 Dihedral : 8.188 81.953 8208 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.85 % Favored : 99.14 % Rotamer: Outliers : 2.11 % Allowed : 19.04 % Favored : 78.86 % 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: 0.98 (0.09), residues: 7294 helix: 1.44 (0.08), residues: 4130 sheet: 0.50 (0.15), residues: 826 loop : -0.64 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 401 PHE 0.013 0.001 PHE M 44 TYR 0.010 0.001 TYR K 506 ARG 0.008 0.000 ARG E 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 414 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 295 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1739 (pp-130) cc_final: 0.1023 (tmt) REVERT: A 267 MET cc_start: 0.1797 (OUTLIER) cc_final: 0.1099 (pp-130) REVERT: C 233 MET cc_start: 0.5395 (tmt) cc_final: 0.5116 (pp-130) REVERT: D 76 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8417 (tp30) REVERT: D 193 MET cc_start: 0.5137 (tpt) cc_final: 0.4841 (tmt) REVERT: E 233 MET cc_start: 0.6373 (tmt) cc_final: 0.6111 (pmt) REVERT: E 267 MET cc_start: 0.1302 (OUTLIER) cc_final: 0.0609 (pp-130) REVERT: E 288 MET cc_start: 0.6460 (mmm) cc_final: 0.5117 (ppp) REVERT: F 267 MET cc_start: 0.0957 (OUTLIER) cc_final: 0.0277 (pp-130) REVERT: F 288 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.4759 (ppp) REVERT: H 288 MET cc_start: 0.5782 (mmp) cc_final: 0.4401 (pp-130) REVERT: I 233 MET cc_start: 0.4992 (tmt) cc_final: 0.4746 (pp-130) REVERT: K 76 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: K 193 MET cc_start: 0.4729 (tpt) cc_final: 0.4500 (tpt) REVERT: L 75 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9011 (ttmt) REVERT: L 233 MET cc_start: 0.1686 (OUTLIER) cc_final: 0.0170 (pmt) REVERT: L 267 MET cc_start: 0.1538 (OUTLIER) cc_final: 0.0796 (pp-130) REVERT: N 111 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7947 (mtt) REVERT: N 272 LYS cc_start: 0.3837 (OUTLIER) cc_final: 0.1897 (mttm) outliers start: 119 outliers final: 42 residues processed: 392 average time/residue: 1.3181 time to fit residues: 664.1753 Evaluate side-chains 342 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 289 time to evaluate : 4.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 75 LYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 272 LYS Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 2.9990 chunk 399 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 523 optimal weight: 0.8980 chunk 290 optimal weight: 30.0000 chunk 600 optimal weight: 7.9990 chunk 486 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 359 optimal weight: 0.5980 chunk 631 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 366 GLN J 37 ASN J 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 54726 Z= 0.163 Angle : 0.440 10.849 73990 Z= 0.239 Chirality : 0.039 0.214 8974 Planarity : 0.002 0.050 9618 Dihedral : 7.769 79.659 8206 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.88 % Favored : 99.11 % Rotamer: Outliers : 1.61 % Allowed : 19.71 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.10), residues: 7294 helix: 1.60 (0.08), residues: 4144 sheet: 0.60 (0.15), residues: 826 loop : -0.61 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.017 0.001 PHE J 219 TYR 0.007 0.001 TYR A 478 ARG 0.008 0.000 ARG E 362 *********************** 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 387 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 296 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1741 (pp-130) cc_final: 0.1080 (tmt) REVERT: A 267 MET cc_start: 0.1816 (OUTLIER) cc_final: 0.1141 (pp-130) REVERT: C 267 MET cc_start: -0.0428 (mtt) cc_final: -0.1952 (ppp) REVERT: D 76 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: D 185 ASP cc_start: 0.7898 (m-30) cc_final: 0.7501 (m-30) REVERT: D 193 MET cc_start: 0.5061 (tpt) cc_final: 0.4833 (tmt) REVERT: E 233 MET cc_start: 0.6329 (tmt) cc_final: 0.6110 (pmt) REVERT: E 267 MET cc_start: 0.1315 (OUTLIER) cc_final: 0.0617 (pp-130) REVERT: E 288 MET cc_start: 0.6306 (mmm) cc_final: 0.5176 (ppp) REVERT: F 267 MET cc_start: 0.0970 (OUTLIER) cc_final: 0.0293 (pp-130) REVERT: F 288 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.4786 (ppp) REVERT: H 288 MET cc_start: 0.5837 (mmp) cc_final: 0.4622 (pp-130) REVERT: I 233 MET cc_start: 0.5238 (tmt) cc_final: 0.4795 (pp-130) REVERT: J 76 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: K 76 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: K 233 MET cc_start: 0.3636 (tmt) cc_final: 0.3407 (pp-130) REVERT: L 267 MET cc_start: 0.1530 (OUTLIER) cc_final: 0.0788 (pp-130) REVERT: N 73 MET cc_start: 0.8843 (mtm) cc_final: 0.8610 (mtm) REVERT: N 111 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8117 (mtp) REVERT: N 267 MET cc_start: 0.1232 (OUTLIER) cc_final: 0.0035 (pp-130) outliers start: 91 outliers final: 29 residues processed: 373 average time/residue: 1.3069 time to fit residues: 627.3795 Evaluate side-chains 332 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 293 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 0.2980 chunk 633 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 413 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 704 optimal weight: 10.0000 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 54726 Z= 0.285 Angle : 0.481 10.920 73990 Z= 0.260 Chirality : 0.041 0.137 8974 Planarity : 0.003 0.048 9618 Dihedral : 8.061 82.028 8203 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.82 % Favored : 99.16 % Rotamer: Outliers : 1.52 % Allowed : 19.92 % Favored : 78.55 % 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: 1.08 (0.10), residues: 7294 helix: 1.53 (0.08), residues: 4130 sheet: 0.54 (0.15), residues: 826 loop : -0.63 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.022 0.001 PHE N 219 TYR 0.011 0.001 TYR K 506 ARG 0.008 0.000 ARG E 362 *********************** 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 376 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 290 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1650 (pp-130) cc_final: 0.0961 (tmt) REVERT: A 267 MET cc_start: 0.1793 (OUTLIER) cc_final: 0.1135 (pp-130) REVERT: B 185 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: B 233 MET cc_start: 0.2702 (tmt) cc_final: 0.2395 (pp-130) REVERT: C 267 MET cc_start: 0.0036 (mtt) cc_final: -0.1639 (ppp) REVERT: D 76 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8391 (tp30) REVERT: D 193 MET cc_start: 0.5087 (tpt) cc_final: 0.4852 (tmt) REVERT: E 267 MET cc_start: 0.1338 (OUTLIER) cc_final: 0.0631 (pp-130) REVERT: E 288 MET cc_start: 0.6407 (mmm) cc_final: 0.5388 (ppp) REVERT: F 76 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: F 255 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.3445 (tp30) REVERT: F 267 MET cc_start: 0.0936 (OUTLIER) cc_final: 0.0252 (pp-130) REVERT: F 288 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.4864 (ppp) REVERT: H 288 MET cc_start: 0.5933 (mmp) cc_final: 0.4614 (pp-130) REVERT: I 233 MET cc_start: 0.5333 (tmt) cc_final: 0.5009 (pp-130) REVERT: J 76 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: K 76 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: L 233 MET cc_start: 0.1710 (pmt) cc_final: 0.1381 (pp-130) REVERT: L 267 MET cc_start: 0.1554 (OUTLIER) cc_final: 0.0803 (pp-130) REVERT: N 111 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7950 (mtt) REVERT: N 267 MET cc_start: 0.1172 (OUTLIER) cc_final: 0.0083 (pp-130) outliers start: 86 outliers final: 36 residues processed: 359 average time/residue: 1.3129 time to fit residues: 608.7412 Evaluate side-chains 338 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 289 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 44 PHE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 401 optimal weight: 0.5980 chunk 514 optimal weight: 0.5980 chunk 398 optimal weight: 30.0000 chunk 592 optimal weight: 1.9990 chunk 393 optimal weight: 20.0000 chunk 701 optimal weight: 6.9990 chunk 439 optimal weight: 50.0000 chunk 427 optimal weight: 0.6980 chunk 323 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0736 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= 0.150 Angle : 0.435 10.782 73990 Z= 0.236 Chirality : 0.039 0.139 8974 Planarity : 0.002 0.048 9618 Dihedral : 7.626 78.891 8203 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.96 % Favored : 99.03 % Rotamer: Outliers : 1.19 % Allowed : 20.40 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 7294 helix: 1.69 (0.08), residues: 4144 sheet: 0.23 (0.14), residues: 1176 loop : -0.37 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.020 0.001 PHE H 219 TYR 0.007 0.001 TYR A 478 ARG 0.008 0.000 ARG E 362 *********************** 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 363 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 296 time to evaluate : 4.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1618 (pp-130) cc_final: 0.0963 (tmt) REVERT: B 233 MET cc_start: 0.2787 (tmt) cc_final: 0.2457 (pp-130) REVERT: C 267 MET cc_start: 0.0022 (mtt) cc_final: -0.1628 (ppp) REVERT: D 76 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: E 267 MET cc_start: 0.1301 (OUTLIER) cc_final: 0.0603 (pp-130) REVERT: E 288 MET cc_start: 0.6435 (mmm) cc_final: 0.5472 (ppp) REVERT: E 404 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6898 (mpt-90) REVERT: F 76 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: F 111 MET cc_start: 0.8473 (mtp) cc_final: 0.8259 (mtt) REVERT: F 267 MET cc_start: 0.0767 (OUTLIER) cc_final: 0.0092 (pp-130) REVERT: F 288 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.4856 (ppp) REVERT: H 288 MET cc_start: 0.5874 (mmp) cc_final: 0.4608 (pp-130) REVERT: J 288 MET cc_start: 0.4157 (mmm) cc_final: 0.3859 (ppp) REVERT: K 76 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: K 233 MET cc_start: 0.1014 (OUTLIER) cc_final: -0.0625 (tmt) REVERT: L 233 MET cc_start: 0.1696 (pmt) cc_final: 0.1385 (pp-130) REVERT: L 267 MET cc_start: 0.1604 (OUTLIER) cc_final: 0.0839 (pp-130) REVERT: L 288 MET cc_start: 0.4906 (mmp) cc_final: 0.4129 (ppp) REVERT: N 267 MET cc_start: 0.1171 (OUTLIER) cc_final: 0.0013 (pp-130) outliers start: 67 outliers final: 18 residues processed: 348 average time/residue: 1.3438 time to fit residues: 600.7261 Evaluate side-chains 320 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 267 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 7.9990 chunk 280 optimal weight: 30.0000 chunk 419 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 135 optimal weight: 50.0000 chunk 446 optimal weight: 6.9990 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 0.0070 chunk 65 optimal weight: 0.8980 chunk 551 optimal weight: 50.0000 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 366 GLN J 366 GLN N 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 54726 Z= 0.235 Angle : 0.467 11.019 73990 Z= 0.251 Chirality : 0.040 0.378 8974 Planarity : 0.003 0.047 9618 Dihedral : 7.833 80.341 8200 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.80 % Favored : 99.19 % Rotamer: Outliers : 1.06 % Allowed : 20.51 % Favored : 78.43 % 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: 1.25 (0.10), residues: 7294 helix: 1.64 (0.08), residues: 4130 sheet: 0.21 (0.14), residues: 1176 loop : -0.37 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.018 0.001 PHE B 44 TYR 0.009 0.001 TYR K 506 ARG 0.008 0.000 ARG E 362 *********************** 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 353 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 193 MET cc_start: 0.4992 (tpt) cc_final: 0.4386 (tmt) REVERT: G 233 MET cc_start: 0.1578 (pp-130) cc_final: 0.0910 (tmt) REVERT: C 267 MET cc_start: 0.0033 (mtt) cc_final: -0.1625 (ppp) REVERT: D 76 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: E 233 MET cc_start: 0.2850 (OUTLIER) cc_final: 0.1923 (pmt) REVERT: E 267 MET cc_start: 0.1321 (OUTLIER) cc_final: 0.0619 (pp-130) REVERT: E 288 MET cc_start: 0.6395 (mmm) cc_final: 0.5475 (ppp) REVERT: F 76 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: F 288 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.4846 (ppp) REVERT: I 233 MET cc_start: 0.5416 (tmt) cc_final: 0.4431 (pp-130) REVERT: J 76 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: J 288 MET cc_start: 0.4422 (mmm) cc_final: 0.4120 (ppp) REVERT: K 76 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: K 233 MET cc_start: 0.0856 (OUTLIER) cc_final: -0.0765 (tmt) REVERT: K 307 MET cc_start: -0.0930 (tmt) cc_final: -0.1185 (tmt) REVERT: L 75 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8875 (ttmt) REVERT: L 233 MET cc_start: 0.1702 (pmt) cc_final: 0.1412 (pp-130) REVERT: L 267 MET cc_start: 0.1438 (OUTLIER) cc_final: 0.0667 (pp-130) REVERT: L 288 MET cc_start: 0.4857 (mmp) cc_final: 0.4288 (ppp) REVERT: N 267 MET cc_start: 0.1172 (OUTLIER) cc_final: 0.0121 (pp-130) outliers start: 60 outliers final: 26 residues processed: 342 average time/residue: 1.3577 time to fit residues: 596.5143 Evaluate side-chains 327 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 290 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 75 LYS Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 0.9990 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 2.9990 chunk 653 optimal weight: 50.0000 chunk 393 optimal weight: 50.0000 chunk 284 optimal weight: 0.3980 chunk 513 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 590 optimal weight: 5.9990 chunk 618 optimal weight: 1.9990 chunk 651 optimal weight: 20.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN N 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 54726 Z= 0.246 Angle : 0.474 12.107 73990 Z= 0.255 Chirality : 0.040 0.261 8974 Planarity : 0.003 0.046 9618 Dihedral : 7.923 80.884 8199 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.90 % Favored : 99.08 % Rotamer: Outliers : 0.89 % Allowed : 20.70 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 7294 helix: 1.60 (0.08), residues: 4130 sheet: 0.20 (0.14), residues: 1176 loop : -0.37 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.017 0.002 PHE B 44 TYR 0.009 0.001 TYR K 506 ARG 0.008 0.000 ARG E 362 *********************** 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 339 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 289 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 193 MET cc_start: 0.5089 (tpt) cc_final: 0.4488 (tmt) REVERT: G 233 MET cc_start: 0.1619 (pp-130) cc_final: 0.0844 (tmt) REVERT: A 193 MET cc_start: 0.5724 (tpt) cc_final: 0.4998 (tmt) REVERT: B 233 MET cc_start: 0.2758 (tmt) cc_final: 0.2158 (ptt) REVERT: C 267 MET cc_start: 0.0107 (mtt) cc_final: -0.1607 (ppp) REVERT: D 76 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8388 (tp30) REVERT: E 267 MET cc_start: 0.1406 (OUTLIER) cc_final: 0.0695 (pp-130) REVERT: E 288 MET cc_start: 0.6458 (mmm) cc_final: 0.5559 (ppp) REVERT: F 76 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: F 288 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.4856 (ppp) REVERT: H 288 MET cc_start: 0.5807 (mmp) cc_final: 0.4401 (pp-130) REVERT: I 233 MET cc_start: 0.5435 (tmt) cc_final: 0.4322 (ppp) REVERT: J 76 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: J 267 MET cc_start: 0.0965 (OUTLIER) cc_final: -0.0520 (pp-130) REVERT: J 288 MET cc_start: 0.4499 (mmm) cc_final: 0.4283 (ppp) REVERT: K 76 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: K 233 MET cc_start: 0.0841 (OUTLIER) cc_final: -0.0564 (tmt) REVERT: L 233 MET cc_start: 0.1640 (pmt) cc_final: 0.1386 (pp-130) REVERT: L 267 MET cc_start: 0.1436 (OUTLIER) cc_final: 0.0652 (pp-130) REVERT: L 288 MET cc_start: 0.5068 (mmp) cc_final: 0.4492 (ppp) REVERT: N 267 MET cc_start: 0.1115 (OUTLIER) cc_final: 0.0070 (pp-130) outliers start: 50 outliers final: 27 residues processed: 331 average time/residue: 1.3646 time to fit residues: 582.6619 Evaluate side-chains 325 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 288 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.9990 chunk 691 optimal weight: 10.0000 chunk 422 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 480 optimal weight: 0.9990 chunk 725 optimal weight: 3.9990 chunk 667 optimal weight: 0.8980 chunk 577 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 446 optimal weight: 7.9990 chunk 354 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 54726 Z= 0.178 Angle : 0.457 12.748 73990 Z= 0.244 Chirality : 0.039 0.207 8974 Planarity : 0.002 0.045 9618 Dihedral : 7.684 78.883 8199 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.86 % Favored : 99.12 % Rotamer: Outliers : 0.90 % Allowed : 20.65 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.10), residues: 7294 helix: 1.67 (0.08), residues: 4144 sheet: 0.24 (0.14), residues: 1176 loop : -0.37 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.019 0.001 PHE D 44 TYR 0.007 0.001 TYR A 478 ARG 0.007 0.000 ARG E 362 ********************** 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 343 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 5.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 193 MET cc_start: 0.5265 (tpt) cc_final: 0.4680 (tmt) REVERT: G 233 MET cc_start: 0.1520 (pp-130) cc_final: 0.0775 (tmt) REVERT: A 193 MET cc_start: 0.5646 (tpt) cc_final: 0.4915 (tmt) REVERT: B 233 MET cc_start: 0.2978 (tmt) cc_final: 0.2382 (ptt) REVERT: C 267 MET cc_start: 0.0079 (mtt) cc_final: -0.1615 (ppp) REVERT: C 288 MET cc_start: 0.5881 (mmp) cc_final: 0.4261 (pp-130) REVERT: D 76 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: E 267 MET cc_start: 0.1406 (OUTLIER) cc_final: 0.0694 (pp-130) REVERT: E 288 MET cc_start: 0.6445 (mmm) cc_final: 0.5563 (ppp) REVERT: F 76 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: F 288 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.4866 (ppp) REVERT: H 288 MET cc_start: 0.5720 (mmp) cc_final: 0.4433 (pp-130) REVERT: I 193 MET cc_start: 0.4527 (tpp) cc_final: 0.4080 (tpt) REVERT: I 233 MET cc_start: 0.5355 (tmt) cc_final: 0.4302 (ppp) REVERT: J 76 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: J 267 MET cc_start: 0.0956 (OUTLIER) cc_final: -0.0536 (pp-130) REVERT: K 76 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: K 233 MET cc_start: 0.0819 (OUTLIER) cc_final: -0.0543 (tmt) REVERT: K 288 MET cc_start: 0.5127 (mmm) cc_final: 0.4434 (ppp) REVERT: L 233 MET cc_start: 0.1690 (pmt) cc_final: 0.1456 (pp-130) REVERT: L 267 MET cc_start: 0.1419 (OUTLIER) cc_final: 0.0640 (pp-130) REVERT: L 288 MET cc_start: 0.5025 (mmp) cc_final: 0.4518 (ppp) REVERT: N 267 MET cc_start: 0.1120 (OUTLIER) cc_final: 0.0069 (pp-130) outliers start: 51 outliers final: 25 residues processed: 334 average time/residue: 1.3609 time to fit residues: 581.1793 Evaluate side-chains 325 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain N residue 467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 0.0370 chunk 615 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 532 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 578 optimal weight: 0.6980 chunk 242 optimal weight: 9.9990 chunk 593 optimal weight: 0.0000 chunk 73 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN F 37 ASN I 37 ASN J 366 GLN N 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.182992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125893 restraints weight = 68138.118| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.96 r_work: 0.3177 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 54726 Z= 0.129 Angle : 0.439 12.038 73990 Z= 0.234 Chirality : 0.038 0.185 8974 Planarity : 0.002 0.043 9618 Dihedral : 7.374 78.820 8196 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.88 % Favored : 99.11 % Rotamer: Outliers : 0.67 % Allowed : 20.84 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.10), residues: 7294 helix: 1.77 (0.08), residues: 4158 sheet: 0.30 (0.14), residues: 1176 loop : -0.35 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS M 401 PHE 0.022 0.001 PHE G 195 TYR 0.007 0.001 TYR A 478 ARG 0.007 0.000 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12491.07 seconds wall clock time: 221 minutes 32.02 seconds (13292.02 seconds total)