Starting phenix.real_space_refine on Tue Feb 13 13:16:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bly_16115/02_2024/8bly_16115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bly_16115/02_2024/8bly_16115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bly_16115/02_2024/8bly_16115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bly_16115/02_2024/8bly_16115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bly_16115/02_2024/8bly_16115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bly_16115/02_2024/8bly_16115_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.012 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: 6 Type Number sf(0) Gaussians 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 10990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 257": "OE1" <-> "OE2" Residue "H ASP 473": "OD1" <-> "OD2" Residue "H GLU 483": "OE1" <-> "OE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 473": "OD1" <-> "OD2" Residue "I GLU 483": "OE1" <-> "OE2" Residue "J PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ASP 435": "OD1" <-> "OD2" Residue "K TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 473": "OD1" <-> "OD2" Residue "L TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54334 Number of models: 1 Model: "" Number of chains: 28 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: "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: "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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 14 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 G 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: 20.98, per 1000 atoms: 0.39 Number of scatterers: 54334 At special positions: 0 Unit cell: (151.41, 154.35, 163.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 280 16.00 P 42 15.00 Mg 14 11.99 O 10990 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.09 Conformation dependent library (CDL) restraints added in 7.9 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: 281 helices and 98 sheets defined 52.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.74 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 85 removed outlier: 4.028A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 230 through 243 Proline residue: A 235 - end of helix 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 426 removed outlier: 3.757A pdb=" N LEU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 457 removed outlier: 4.050A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.087A 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 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.839A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 65 through 85 removed outlier: 4.114A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.625A 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 231 through 243 Proline residue: B 235 - end of helix 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 424 Processing helix chain 'B' and resid 434 through 457 removed outlier: 4.147A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.976A 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 514 Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.882A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 85 removed outlier: 4.029A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 108 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 156 through 168 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 434 through 457 removed outlier: 4.238A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 4.273A 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 514 Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.853A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.808A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 240 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 426 removed outlier: 3.722A pdb=" N LEU D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 457 removed outlier: 4.078A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.145A 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 515 Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.848A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 85 removed outlier: 4.020A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.775A 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 243 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 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' 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 424 Processing helix chain 'E' and resid 434 through 457 removed outlier: 4.035A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.995A 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 515 Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.914A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.846A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 108 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 230 through 243 Proline residue: F 235 - end of helix 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 424 Processing helix chain 'F' and resid 434 through 457 removed outlier: 4.098A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 4.138A 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 514 Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.905A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.885A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.569A 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 230 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 424 Processing helix chain 'G' and resid 434 through 457 removed outlier: 4.069A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 4.089A 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 514 Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.924A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 5.310A 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: 4.097A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.847A 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 230 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 426 removed outlier: 3.710A pdb=" N LEU H 426 " --> pdb=" O VAL H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 458 removed outlier: 4.013A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 4.108A 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 514 Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.922A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 85 removed outlier: 4.135A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 156 through 168 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 230 through 243 removed outlier: 3.558A pdb=" N LEU I 234 " --> pdb=" O ARG I 231 " (cutoff:3.500A) 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 426 removed outlier: 3.699A pdb=" N LEU I 426 " --> pdb=" O VAL I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 457 removed outlier: 4.015A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 4.105A 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 514 Processing helix chain 'J' and resid 9 through 30 removed outlier: 3.924A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 85 removed outlier: 3.953A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.578A 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 169 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 243 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 424 Processing helix chain 'J' and resid 434 through 457 removed outlier: 4.096A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 4.162A 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 514 Processing helix chain 'K' and resid 9 through 30 removed outlier: 3.838A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 85 removed outlier: 4.010A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.584A 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 231 through 240 Proline residue: K 235 - end of helix 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 424 Processing helix chain 'K' and resid 434 through 457 removed outlier: 4.023A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.979A 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 514 Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.869A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 85 removed outlier: 3.866A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.647A 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 231 through 242 Proline residue: L 235 - end of helix 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 426 removed outlier: 3.710A pdb=" N LEU L 426 " --> pdb=" O VAL L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 457 removed outlier: 4.140A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 4.121A 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 515 Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.878A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 65 through 85 removed outlier: 3.992A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.566A 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 243 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 424 Processing helix chain 'M' and resid 434 through 457 removed outlier: 4.235A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.276A 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 514 Processing helix chain 'N' and resid 9 through 30 removed outlier: 3.834A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 85 removed outlier: 3.824A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.542A 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 243 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 424 Processing helix chain 'N' and resid 434 through 457 removed outlier: 4.137A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.982A 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 514 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.635A pdb=" N VAL A 323 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.987A pdb=" N ALA A 274 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA A 251 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 276 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= K, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.621A pdb=" N VAL B 323 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 222 removed outlier: 6.906A pdb=" N ALA B 274 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA B 251 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 276 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= P, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= Q, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= R, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.605A pdb=" N VAL C 323 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 219 through 222 removed outlier: 6.994A pdb=" N ALA C 274 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ALA C 251 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL C 276 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= U, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= V, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= W, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= X, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= Y, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.587A pdb=" N VAL D 323 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 219 through 222 removed outlier: 7.013A pdb=" N ALA D 274 " --> pdb=" O ILE D 249 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AB, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AC, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AD, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AE, first strand: chain 'E' and resid 175 through 179 removed outlier: 6.264A pdb=" N ALA E 377 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU E 178 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE E 379 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.599A pdb=" N VAL E 323 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 219 through 222 removed outlier: 6.880A pdb=" N ALA E 274 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA E 251 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL E 276 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AI, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AJ, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AK, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AL, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AM, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.594A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 219 through 222 removed outlier: 7.086A pdb=" N ALA F 274 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AP, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AQ, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= AR, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= AS, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= AT, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.602A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 219 through 222 removed outlier: 6.998A pdb=" N ALA G 274 " --> pdb=" O ILE G 249 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= AW, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= AX, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= AY, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= AZ, first strand: chain 'H' and resid 175 through 179 removed outlier: 6.272A pdb=" N ALA H 377 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU H 178 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE H 379 " --> pdb=" O GLU H 178 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 193 through 195 removed outlier: 3.586A pdb=" N VAL H 323 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'H' and resid 219 through 222 removed outlier: 6.867A pdb=" N ALA H 274 " --> pdb=" O ILE H 249 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA H 251 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL H 276 " --> pdb=" O ALA H 251 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BD, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BE, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'I' and resid 193 through 195 removed outlier: 3.727A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'I' and resid 219 through 222 removed outlier: 6.872A pdb=" N ALA I 274 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA I 251 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL I 276 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BL, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BM, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BN, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BO, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.611A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'J' and resid 219 through 222 removed outlier: 7.030A pdb=" N ALA J 274 " --> pdb=" O ILE J 249 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BR, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BS, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BT, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BU, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= BV, first strand: chain 'K' and resid 193 through 195 removed outlier: 3.555A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.947A pdb=" N ALA K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA K 251 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL K 276 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BY, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BZ, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CA, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CB, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CC, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.599A pdb=" N VAL L 323 " --> pdb=" O LEU L 215 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'L' and resid 219 through 222 removed outlier: 6.949A pdb=" N ALA L 274 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ALA L 251 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL L 276 " --> pdb=" O ALA L 251 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CF, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CG, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CH, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CI, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CJ, first strand: chain 'M' and resid 193 through 195 removed outlier: 3.644A pdb=" N VAL M 323 " --> pdb=" O LEU M 215 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'M' and resid 219 through 222 removed outlier: 6.900A pdb=" N ALA M 274 " --> pdb=" O ILE M 249 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CM, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CN, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= CO, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CP, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= CQ, first strand: chain 'N' and resid 193 through 195 removed outlier: 3.696A pdb=" N VAL N 323 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'N' and resid 219 through 222 removed outlier: 6.963A pdb=" N ALA N 274 " --> pdb=" O ILE N 249 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= CT, first strand: chain 'N' and resid 476 through 479 3104 hydrogen bonds defined for protein. 8907 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: 20.22 Time building geometry restraints manager: 18.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18830 1.34 - 1.46: 9364 1.46 - 1.58: 25958 1.58 - 1.70: 56 1.70 - 1.81: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" CB GLU I 484 " pdb=" CG GLU I 484 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB ARG K 362 " pdb=" CG ARG K 362 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.87e-01 bond pdb=" CB MET K 514 " pdb=" CG MET K 514 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.77e-01 bond pdb=" CA VAL D 189 " pdb=" CB VAL D 189 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.74e-01 bond pdb=" CA VAL F 189 " pdb=" CB VAL F 189 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.67e-01 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 96.69 - 105.32: 900 105.32 - 113.96: 33095 113.96 - 122.60: 34505 122.60 - 131.24: 5448 131.24 - 139.88: 42 Bond angle restraints: 73990 Sorted by residual: angle pdb=" CB MET J 111 " pdb=" CG MET J 111 " pdb=" SD MET J 111 " ideal model delta sigma weight residual 112.70 126.45 -13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" CA ARG D 362 " pdb=" CB ARG D 362 " pdb=" CG ARG D 362 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB MET G 488 " pdb=" CG MET G 488 " pdb=" SD MET G 488 " ideal model delta sigma weight residual 112.70 122.37 -9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET F 69 " pdb=" CG MET F 69 " pdb=" SD MET F 69 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.82e+00 angle pdb=" N ILE B 230 " pdb=" CA ILE B 230 " pdb=" C ILE B 230 " ideal model delta sigma weight residual 111.90 109.60 2.30 8.10e-01 1.52e+00 8.08e+00 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 29921 17.88 - 35.77: 3146 35.77 - 53.65: 843 53.65 - 71.53: 190 71.53 - 89.41: 60 Dihedral angle restraints: 34160 sinusoidal: 13510 harmonic: 20650 Sorted by residual: dihedral pdb=" CA THR K 50 " pdb=" C THR K 50 " pdb=" N LYS K 51 " pdb=" CA LYS K 51 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP N 196 " pdb=" CB ASP N 196 " pdb=" CG ASP N 196 " pdb=" OD1 ASP N 196 " ideal model delta sinusoidal sigma weight residual -30.00 -84.78 54.78 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP J 196 " pdb=" CB ASP J 196 " pdb=" CG ASP J 196 " pdb=" OD1 ASP J 196 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 5606 0.027 - 0.054: 1894 0.054 - 0.080: 872 0.080 - 0.107: 443 0.107 - 0.134: 159 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CA VAL L 136 " pdb=" N VAL L 136 " pdb=" C VAL L 136 " pdb=" CB VAL L 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL I 136 " pdb=" N VAL I 136 " pdb=" C VAL I 136 " pdb=" CB VAL I 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL E 136 " pdb=" N VAL E 136 " pdb=" C VAL E 136 " pdb=" CB VAL E 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 362 " 0.124 9.50e-02 1.11e+02 5.61e-02 2.41e+00 pdb=" NE ARG D 362 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 362 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 362 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 362 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 449 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 450 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 450 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 450 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 449 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO M 450 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO M 450 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 450 " -0.019 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 400 2.56 - 3.14: 43741 3.14 - 3.73: 91377 3.73 - 4.31: 123366 4.31 - 4.90: 206959 Nonbonded interactions: 465843 Sorted by model distance: nonbonded pdb="MG MG M 601 " pdb=" O2A ATP M 602 " model vdw 1.971 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2A ATP C 602 " model vdw 1.972 2.170 nonbonded pdb="MG MG C 601 " pdb=" O3G ATP C 602 " model vdw 1.976 2.170 nonbonded pdb="MG MG M 601 " pdb=" O3G ATP M 602 " model vdw 1.977 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2A ATP B 602 " model vdw 1.978 2.170 ... (remaining 465838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 5.650 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 112.870 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.002 0.032 54726 Z= 0.156 Angle : 0.466 13.747 73990 Z= 0.255 Chirality : 0.039 0.134 8974 Planarity : 0.002 0.056 9618 Dihedral : 16.452 89.414 20916 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.18 % Allowed : 18.03 % Favored : 81.80 % 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: 1.71 (0.08), residues: 4088 sheet: 0.46 (0.14), residues: 1176 loop : -0.57 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.008 0.001 PHE I 195 TYR 0.018 0.001 TYR I 203 ARG 0.012 0.000 ARG D 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 253 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 243 time to evaluate : 4.652 Fit side-chains revert: symmetry clash REVERT: C 193 MET cc_start: 0.7001 (tpp) cc_final: 0.6708 (tpt) REVERT: C 307 MET cc_start: 0.6875 (tpt) cc_final: 0.6550 (tpt) REVERT: L 362 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6681 (tmm160) outliers start: 10 outliers final: 2 residues processed: 249 average time/residue: 0.4868 time to fit residues: 214.2611 Evaluate side-chains 245 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 4.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain L residue 362 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 3.9990 chunk 551 optimal weight: 0.0270 chunk 306 optimal weight: 6.9990 chunk 188 optimal weight: 30.0000 chunk 372 optimal weight: 0.0370 chunk 294 optimal weight: 40.0000 chunk 570 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 346 optimal weight: 40.0000 chunk 424 optimal weight: 8.9990 chunk 661 optimal weight: 5.9990 overall best weight: 1.1118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN C 366 GLN F 37 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 54726 Z= 0.160 Angle : 0.439 10.209 73990 Z= 0.238 Chirality : 0.039 0.159 8974 Planarity : 0.002 0.034 9618 Dihedral : 7.552 87.391 8196 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.42 % Allowed : 17.46 % Favored : 81.12 % 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: 1.44 (0.10), residues: 7294 helix: 1.88 (0.08), residues: 4102 sheet: 0.36 (0.14), residues: 1176 loop : -0.55 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.007 0.001 PHE M 8 TYR 0.008 0.001 TYR N 478 ARG 0.005 0.000 ARG D 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 323 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 243 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: B 63 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: B 233 MET cc_start: 0.1565 (ppp) cc_final: 0.0779 (ptp) REVERT: D 227 ILE cc_start: 0.3272 (OUTLIER) cc_final: 0.2673 (mm) REVERT: E 193 MET cc_start: 0.6238 (tpt) cc_final: 0.5909 (tpt) REVERT: G 63 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: I 366 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5885 (pp30) REVERT: K 233 MET cc_start: 0.2145 (ppp) cc_final: 0.1588 (ptm) REVERT: L 362 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6666 (tmm160) REVERT: L 483 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: N 63 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: N 193 MET cc_start: 0.7300 (tpp) cc_final: 0.7084 (tpt) REVERT: N 362 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6473 (ptt90) outliers start: 80 outliers final: 31 residues processed: 306 average time/residue: 0.4943 time to fit residues: 265.9160 Evaluate side-chains 282 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 550 optimal weight: 10.0000 chunk 450 optimal weight: 40.0000 chunk 182 optimal weight: 50.0000 chunk 662 optimal weight: 6.9990 chunk 715 optimal weight: 7.9990 chunk 589 optimal weight: 3.9990 chunk 656 optimal weight: 40.0000 chunk 225 optimal weight: 8.9990 chunk 531 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 54726 Z= 0.371 Angle : 0.506 10.047 73990 Z= 0.269 Chirality : 0.042 0.147 8974 Planarity : 0.003 0.040 9618 Dihedral : 8.010 88.250 8195 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.23 % Allowed : 17.35 % Favored : 80.41 % 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: 1.02 (0.10), residues: 7294 helix: 1.50 (0.08), residues: 4130 sheet: 0.34 (0.13), residues: 1162 loop : -0.76 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 401 PHE 0.010 0.001 PHE M 8 TYR 0.008 0.001 TYR G 478 ARG 0.004 0.000 ARG H 395 *********************** 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 372 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 246 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: C 193 MET cc_start: 0.7017 (tpt) cc_final: 0.6658 (tpt) REVERT: C 484 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7981 (pp20) REVERT: D 227 ILE cc_start: 0.3225 (OUTLIER) cc_final: 0.2657 (mm) REVERT: E 193 MET cc_start: 0.6287 (tpt) cc_final: 0.5838 (tpt) REVERT: J 193 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.5983 (tmm) REVERT: J 520 MET cc_start: 0.8944 (mtp) cc_final: 0.8701 (mtp) REVERT: K 233 MET cc_start: 0.2083 (ppp) cc_final: 0.1576 (ptm) REVERT: L 304 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: L 362 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6651 (tmm160) REVERT: L 467 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8628 (t0) REVERT: L 483 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: L 517 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9141 (p) REVERT: M 484 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7879 (pp20) REVERT: N 63 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: N 362 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6617 (tmm160) outliers start: 126 outliers final: 73 residues processed: 356 average time/residue: 0.4817 time to fit residues: 302.3314 Evaluate side-chains 330 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 245 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 0.0040 chunk 497 optimal weight: 50.0000 chunk 343 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 316 optimal weight: 1.9990 chunk 444 optimal weight: 40.0000 chunk 664 optimal weight: 3.9990 chunk 703 optimal weight: 50.0000 chunk 347 optimal weight: 8.9990 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 54726 Z= 0.315 Angle : 0.478 10.204 73990 Z= 0.256 Chirality : 0.041 0.145 8974 Planarity : 0.003 0.034 9618 Dihedral : 7.705 89.350 8195 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.57 % Allowed : 17.72 % Favored : 79.71 % 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: 0.96 (0.10), residues: 7294 helix: 1.47 (0.08), residues: 4130 sheet: 0.26 (0.13), residues: 1162 loop : -0.79 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 401 PHE 0.009 0.001 PHE C 8 TYR 0.008 0.001 TYR A 478 ARG 0.003 0.000 ARG G 421 *********************** 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 390 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 245 time to evaluate : 4.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.4829 (p0) REVERT: C 193 MET cc_start: 0.7384 (tpt) cc_final: 0.6964 (tpt) REVERT: D 63 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: D 227 ILE cc_start: 0.3215 (OUTLIER) cc_final: 0.2648 (mm) REVERT: E 193 MET cc_start: 0.6197 (tpt) cc_final: 0.5785 (tpt) REVERT: F 483 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: G 484 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: H 484 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7873 (pp20) REVERT: I 233 MET cc_start: 0.4490 (ppp) cc_final: 0.3648 (ptp) REVERT: J 140 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.5253 (p0) REVERT: J 483 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: J 520 MET cc_start: 0.9108 (mtp) cc_final: 0.8834 (mtp) REVERT: K 233 MET cc_start: 0.1968 (ppp) cc_final: 0.1546 (ptm) REVERT: L 63 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: L 166 MET cc_start: 0.8911 (mtt) cc_final: 0.8691 (mmm) REVERT: L 193 MET cc_start: 0.6489 (tpt) cc_final: 0.6230 (tpp) REVERT: L 304 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: L 362 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6475 (ppt170) REVERT: L 467 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8512 (t0) REVERT: L 517 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9115 (p) REVERT: M 140 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.5614 (p0) REVERT: M 378 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8691 (p) REVERT: M 484 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7855 (pp20) REVERT: N 63 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: N 193 MET cc_start: 0.6333 (tpt) cc_final: 0.5953 (tpt) REVERT: N 362 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6679 (tmm160) outliers start: 145 outliers final: 83 residues processed: 371 average time/residue: 0.4762 time to fit residues: 313.2173 Evaluate side-chains 346 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 245 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 467 ASN Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 502 SER Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 473 ASP Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 0.9990 chunk 399 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 523 optimal weight: 0.9990 chunk 290 optimal weight: 0.0020 chunk 600 optimal weight: 10.0000 chunk 486 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 631 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 366 GLN M 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 54726 Z= 0.135 Angle : 0.418 8.435 73990 Z= 0.226 Chirality : 0.039 0.141 8974 Planarity : 0.002 0.030 9618 Dihedral : 6.874 87.797 8195 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.91 % Allowed : 18.22 % Favored : 79.87 % 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: 1.38 (0.10), residues: 7294 helix: 1.91 (0.08), residues: 4088 sheet: 0.29 (0.14), residues: 1148 loop : -0.70 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 401 PHE 0.006 0.001 PHE G 8 TYR 0.009 0.001 TYR L 478 ARG 0.002 0.000 ARG I 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 353 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 245 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.4794 (p0) REVERT: B 447 MET cc_start: 0.9171 (mtm) cc_final: 0.8961 (mtt) REVERT: C 467 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 514 MET cc_start: 0.9179 (ttm) cc_final: 0.8711 (ttp) REVERT: D 63 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: D 227 ILE cc_start: 0.3249 (OUTLIER) cc_final: 0.2770 (mm) REVERT: E 161 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8636 (mp) REVERT: E 193 MET cc_start: 0.6328 (tpt) cc_final: 0.6064 (tpt) REVERT: E 301 ILE cc_start: -0.3771 (OUTLIER) cc_final: -0.4018 (tt) REVERT: E 514 MET cc_start: 0.9102 (mtp) cc_final: 0.8877 (ttm) REVERT: F 140 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.5998 (p0) REVERT: F 483 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: G 140 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.5232 (p0) REVERT: G 389 MET cc_start: 0.7854 (tpp) cc_final: 0.7241 (tpp) REVERT: H 272 LYS cc_start: 0.3409 (OUTLIER) cc_final: 0.3189 (tttp) REVERT: I 233 MET cc_start: 0.4465 (ppp) cc_final: 0.3717 (ptp) REVERT: I 362 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6734 (tmm160) REVERT: J 69 MET cc_start: 0.9269 (mtt) cc_final: 0.9052 (mtt) REVERT: J 140 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.5562 (p0) REVERT: J 227 ILE cc_start: 0.0614 (OUTLIER) cc_final: 0.0390 (pp) REVERT: J 483 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: K 233 MET cc_start: 0.1922 (ppp) cc_final: 0.1588 (ptm) REVERT: L 304 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: L 362 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6413 (ppt170) REVERT: M 111 MET cc_start: 0.8868 (mmp) cc_final: 0.8629 (mmm) REVERT: N 193 MET cc_start: 0.6356 (tpt) cc_final: 0.6068 (tpt) REVERT: N 362 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6500 (ptt90) REVERT: N 447 MET cc_start: 0.9035 (mtm) cc_final: 0.8819 (mtt) outliers start: 108 outliers final: 64 residues processed: 344 average time/residue: 0.5059 time to fit residues: 304.3635 Evaluate side-chains 327 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 246 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 272 LYS Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 362 ARG Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 8.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 413 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 30.0000 chunk 584 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 369 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 54726 Z= 0.170 Angle : 0.424 8.560 73990 Z= 0.227 Chirality : 0.039 0.139 8974 Planarity : 0.002 0.030 9618 Dihedral : 6.894 87.581 8195 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.30 % Allowed : 18.10 % Favored : 79.60 % 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: 1.43 (0.10), residues: 7294 helix: 1.96 (0.08), residues: 4088 sheet: 0.31 (0.14), residues: 1148 loop : -0.70 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.006 0.001 PHE K 8 TYR 0.008 0.001 TYR L 478 ARG 0.002 0.000 ARG I 421 *********************** 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: 130 poor density : 246 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.5033 (p0) REVERT: B 447 MET cc_start: 0.9141 (mtm) cc_final: 0.8892 (mtt) REVERT: B 483 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: C 193 MET cc_start: 0.6775 (tpt) cc_final: 0.6281 (tpt) REVERT: C 467 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8514 (t0) REVERT: D 63 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: D 227 ILE cc_start: 0.3221 (OUTLIER) cc_final: 0.2746 (mm) REVERT: D 467 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8566 (t0) REVERT: E 193 MET cc_start: 0.6333 (tpt) cc_final: 0.6044 (tpt) REVERT: E 301 ILE cc_start: -0.3743 (OUTLIER) cc_final: -0.4059 (tt) REVERT: E 514 MET cc_start: 0.9199 (mtp) cc_final: 0.8914 (ttm) REVERT: F 140 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.5981 (p0) REVERT: F 483 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: G 140 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.5481 (p0) REVERT: G 233 MET cc_start: 0.3796 (ppp) cc_final: 0.3592 (ppp) REVERT: G 389 MET cc_start: 0.7824 (tpp) cc_final: 0.7465 (tpp) REVERT: I 233 MET cc_start: 0.4434 (ppp) cc_final: 0.3695 (ptp) REVERT: J 140 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.5383 (p0) REVERT: J 227 ILE cc_start: 0.0591 (OUTLIER) cc_final: 0.0353 (pp) REVERT: J 483 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: L 63 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: L 193 MET cc_start: 0.6440 (tpt) cc_final: 0.6168 (tpt) REVERT: L 304 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: L 362 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6401 (ppt170) REVERT: L 467 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8475 (t0) REVERT: N 193 MET cc_start: 0.6189 (tpt) cc_final: 0.5920 (tpt) REVERT: N 447 MET cc_start: 0.9056 (mtm) cc_final: 0.8774 (mtt) REVERT: N 483 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8016 (mm-30) outliers start: 130 outliers final: 83 residues processed: 362 average time/residue: 0.4860 time to fit residues: 310.0734 Evaluate side-chains 347 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 246 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 483 GLU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 401 optimal weight: 5.9990 chunk 514 optimal weight: 0.9990 chunk 398 optimal weight: 0.9990 chunk 592 optimal weight: 30.0000 chunk 393 optimal weight: 40.0000 chunk 701 optimal weight: 0.8980 chunk 439 optimal weight: 7.9990 chunk 427 optimal weight: 6.9990 chunk 323 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: C 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 54726 Z= 0.142 Angle : 0.417 8.949 73990 Z= 0.223 Chirality : 0.039 0.138 8974 Planarity : 0.002 0.029 9618 Dihedral : 6.645 86.880 8195 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.11 % Allowed : 18.47 % Favored : 79.42 % 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: 1.52 (0.10), residues: 7294 helix: 2.05 (0.08), residues: 4088 sheet: 0.30 (0.14), residues: 1148 loop : -0.68 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.006 0.001 PHE K 8 TYR 0.010 0.001 TYR L 478 ARG 0.005 0.000 ARG N 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 365 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 246 time to evaluate : 4.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.5024 (p0) REVERT: B 447 MET cc_start: 0.9111 (mtm) cc_final: 0.8846 (mtt) REVERT: B 483 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: C 193 MET cc_start: 0.6782 (tpt) cc_final: 0.6329 (tpt) REVERT: C 467 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8496 (t0) REVERT: D 227 ILE cc_start: 0.3158 (OUTLIER) cc_final: 0.2710 (mm) REVERT: D 467 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8537 (t0) REVERT: E 75 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8137 (ttmt) REVERT: E 193 MET cc_start: 0.6116 (tpt) cc_final: 0.5863 (tpt) REVERT: E 301 ILE cc_start: -0.3706 (OUTLIER) cc_final: -0.4085 (tt) REVERT: E 514 MET cc_start: 0.9163 (mtp) cc_final: 0.8911 (ttm) REVERT: F 140 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.6051 (p0) REVERT: F 483 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: G 389 MET cc_start: 0.7863 (tpp) cc_final: 0.7600 (tpp) REVERT: I 233 MET cc_start: 0.4423 (ppp) cc_final: 0.3698 (ptp) REVERT: J 140 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.5362 (p0) REVERT: J 227 ILE cc_start: 0.0560 (OUTLIER) cc_final: 0.0296 (pp) REVERT: J 483 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: K 75 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8063 (ttmt) REVERT: K 467 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8341 (t0) REVERT: L 63 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: L 166 MET cc_start: 0.8917 (mtt) cc_final: 0.8653 (mmm) REVERT: L 193 MET cc_start: 0.6232 (tpt) cc_final: 0.5990 (tpt) REVERT: L 362 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6397 (ppt170) REVERT: M 140 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.5974 (p0) REVERT: M 514 MET cc_start: 0.9127 (ttm) cc_final: 0.8804 (ttp) REVERT: N 193 MET cc_start: 0.6409 (tpt) cc_final: 0.6188 (tpt) REVERT: N 447 MET cc_start: 0.9023 (mtm) cc_final: 0.8728 (mtt) REVERT: N 483 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8015 (mm-30) outliers start: 119 outliers final: 76 residues processed: 356 average time/residue: 0.4835 time to fit residues: 302.9247 Evaluate side-chains 339 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 245 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 467 ASN Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 362 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 483 GLU Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 20.0000 chunk 280 optimal weight: 0.0570 chunk 419 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 137 optimal weight: 50.0000 chunk 135 optimal weight: 0.0270 chunk 446 optimal weight: 7.9990 chunk 478 optimal weight: 0.8980 chunk 346 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 551 optimal weight: 30.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 54726 Z= 0.129 Angle : 0.419 11.836 73990 Z= 0.222 Chirality : 0.038 0.137 8974 Planarity : 0.002 0.028 9618 Dihedral : 6.492 84.907 8195 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.97 % Allowed : 18.50 % Favored : 79.53 % 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: 1.60 (0.10), residues: 7294 helix: 2.12 (0.08), residues: 4088 sheet: 0.33 (0.14), residues: 1148 loop : -0.66 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 401 PHE 0.016 0.001 PHE C 219 TYR 0.009 0.001 TYR L 478 ARG 0.003 0.000 ARG N 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 358 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 247 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.5035 (p0) REVERT: B 447 MET cc_start: 0.9098 (mtm) cc_final: 0.8821 (mtt) REVERT: B 483 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: C 193 MET cc_start: 0.6717 (tpt) cc_final: 0.6288 (tpt) REVERT: C 514 MET cc_start: 0.9175 (ttm) cc_final: 0.8691 (ttp) REVERT: D 227 ILE cc_start: 0.3225 (OUTLIER) cc_final: 0.2756 (mm) REVERT: D 467 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8508 (t0) REVERT: E 75 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8121 (ttmt) REVERT: E 301 ILE cc_start: -0.3691 (OUTLIER) cc_final: -0.4104 (tt) REVERT: E 514 MET cc_start: 0.9160 (mtp) cc_final: 0.8926 (ttm) REVERT: F 140 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6286 (p0) REVERT: G 140 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.5540 (p0) REVERT: I 233 MET cc_start: 0.4158 (ppp) cc_final: 0.3396 (ptp) REVERT: J 140 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.5147 (p0) REVERT: J 227 ILE cc_start: 0.0517 (OUTLIER) cc_final: 0.0268 (pp) REVERT: J 483 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: K 75 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8059 (ttmt) REVERT: K 467 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8482 (t0) REVERT: L 63 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: L 166 MET cc_start: 0.8907 (mtt) cc_final: 0.8666 (mmm) REVERT: M 140 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.5956 (p0) REVERT: M 514 MET cc_start: 0.9113 (ttm) cc_final: 0.8766 (ttp) REVERT: N 193 MET cc_start: 0.6494 (tpt) cc_final: 0.6264 (tpt) REVERT: N 447 MET cc_start: 0.9010 (mtm) cc_final: 0.8727 (mtt) outliers start: 111 outliers final: 82 residues processed: 350 average time/residue: 0.4790 time to fit residues: 297.6569 Evaluate side-chains 342 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 245 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 467 ASN Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 473 ASP Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 2.9990 chunk 672 optimal weight: 10.0000 chunk 613 optimal weight: 3.9990 chunk 653 optimal weight: 50.0000 chunk 393 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 513 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 590 optimal weight: 7.9990 chunk 618 optimal weight: 0.0970 chunk 651 optimal weight: 40.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54726 Z= 0.252 Angle : 0.456 11.657 73990 Z= 0.240 Chirality : 0.040 0.158 8974 Planarity : 0.002 0.028 9618 Dihedral : 6.906 83.179 8191 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.00 % Allowed : 18.56 % Favored : 79.44 % 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: 1.41 (0.10), residues: 7294 helix: 1.91 (0.08), residues: 4088 sheet: 0.34 (0.14), residues: 1148 loop : -0.66 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.009 0.001 PHE C 8 TYR 0.014 0.001 TYR I 203 ARG 0.003 0.000 ARG J 445 *********************** 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 359 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 246 time to evaluate : 4.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.5411 (p0) REVERT: B 483 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: C 193 MET cc_start: 0.6721 (tpt) cc_final: 0.6321 (tpt) REVERT: C 467 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8505 (t0) REVERT: C 514 MET cc_start: 0.9195 (ttm) cc_final: 0.8722 (ttp) REVERT: D 227 ILE cc_start: 0.3350 (OUTLIER) cc_final: 0.2813 (mm) REVERT: D 467 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8586 (t0) REVERT: E 75 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8192 (ttmt) REVERT: E 161 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8663 (mp) REVERT: E 301 ILE cc_start: -0.3616 (OUTLIER) cc_final: -0.4069 (tt) REVERT: F 140 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6037 (p0) REVERT: F 483 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: G 63 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: G 140 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.5606 (p0) REVERT: I 233 MET cc_start: 0.4166 (ppp) cc_final: 0.3407 (ptp) REVERT: J 140 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.5177 (p0) REVERT: J 227 ILE cc_start: 0.0524 (OUTLIER) cc_final: 0.0281 (pp) REVERT: J 483 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: K 75 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8094 (ttmt) REVERT: K 233 MET cc_start: 0.0535 (ppp) cc_final: 0.0329 (ppp) REVERT: K 467 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8387 (t0) REVERT: L 63 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: L 166 MET cc_start: 0.8922 (mtt) cc_final: 0.8666 (mmm) REVERT: L 193 MET cc_start: 0.6717 (tpt) cc_final: 0.6438 (tpp) REVERT: L 467 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8530 (t0) REVERT: M 140 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.5959 (p0) REVERT: M 484 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7836 (pp20) REVERT: M 514 MET cc_start: 0.9144 (ttm) cc_final: 0.8835 (ttp) REVERT: N 193 MET cc_start: 0.6525 (tpt) cc_final: 0.6284 (tpt) REVERT: N 447 MET cc_start: 0.9049 (mtm) cc_final: 0.8783 (mtt) outliers start: 113 outliers final: 84 residues processed: 351 average time/residue: 0.4721 time to fit residues: 294.8936 Evaluate side-chains 351 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 246 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 467 ASN Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 473 ASP Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 4.9990 chunk 691 optimal weight: 6.9990 chunk 422 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 480 optimal weight: 4.9990 chunk 725 optimal weight: 2.9990 chunk 667 optimal weight: 5.9990 chunk 577 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 446 optimal weight: 6.9990 chunk 354 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54726 Z= 0.212 Angle : 0.447 10.905 73990 Z= 0.236 Chirality : 0.039 0.136 8974 Planarity : 0.002 0.029 9618 Dihedral : 6.825 82.571 8191 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.02 % Allowed : 18.50 % Favored : 79.48 % 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: 1.39 (0.10), residues: 7294 helix: 1.89 (0.08), residues: 4088 sheet: 0.32 (0.14), residues: 1148 loop : -0.66 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.007 0.001 PHE M 8 TYR 0.013 0.001 TYR I 203 ARG 0.002 0.000 ARG H 421 ********************** 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 360 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 246 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.5403 (p0) REVERT: B 483 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: C 193 MET cc_start: 0.6660 (tpt) cc_final: 0.6249 (tpt) REVERT: C 467 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8502 (t0) REVERT: C 514 MET cc_start: 0.9177 (ttm) cc_final: 0.8691 (ttp) REVERT: D 227 ILE cc_start: 0.3304 (OUTLIER) cc_final: 0.2792 (mm) REVERT: D 467 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8569 (t0) REVERT: E 75 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8198 (ttmt) REVERT: E 161 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (mp) REVERT: E 301 ILE cc_start: -0.3613 (OUTLIER) cc_final: -0.4062 (tt) REVERT: F 140 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.5756 (p0) REVERT: F 483 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: G 63 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: G 140 ASP cc_start: 0.6349 (OUTLIER) cc_final: 0.5472 (p0) REVERT: I 233 MET cc_start: 0.3072 (ppp) cc_final: 0.2222 (ptp) REVERT: J 140 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.4618 (p0) REVERT: J 227 ILE cc_start: 0.0521 (OUTLIER) cc_final: 0.0287 (pp) REVERT: K 75 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8097 (ttmt) REVERT: K 467 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8384 (t0) REVERT: L 63 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: L 166 MET cc_start: 0.8910 (mtt) cc_final: 0.8674 (mmm) REVERT: L 193 MET cc_start: 0.6382 (tpt) cc_final: 0.6173 (tpp) REVERT: L 467 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8539 (t0) REVERT: M 140 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.5828 (p0) REVERT: M 484 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: M 514 MET cc_start: 0.9139 (ttm) cc_final: 0.8799 (ttp) REVERT: N 193 MET cc_start: 0.6524 (tpt) cc_final: 0.6272 (tpt) outliers start: 114 outliers final: 88 residues processed: 350 average time/residue: 0.4714 time to fit residues: 293.9162 Evaluate side-chains 354 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 246 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 226 LYS Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 353 ILE Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 467 ASN Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 473 ASP Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 1.9990 chunk 615 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 532 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 578 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 593 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091727 restraints weight = 105659.581| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.69 r_work: 0.3024 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54726 Z= 0.268 Angle : 0.471 13.030 73990 Z= 0.247 Chirality : 0.040 0.136 8974 Planarity : 0.002 0.029 9618 Dihedral : 7.102 85.391 8191 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.11 % Allowed : 18.59 % Favored : 79.30 % 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: 1.25 (0.10), residues: 7294 helix: 1.75 (0.08), residues: 4088 sheet: 0.30 (0.14), residues: 1148 loop : -0.67 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.009 0.001 PHE C 8 TYR 0.013 0.001 TYR I 203 ARG 0.003 0.000 ARG I 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8270.99 seconds wall clock time: 149 minutes 2.98 seconds (8942.98 seconds total)