Starting phenix.real_space_refine on Wed Mar 4 17:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vm3_21237/03_2026/6vm3_21237.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vm3_21237/03_2026/6vm3_21237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vm3_21237/03_2026/6vm3_21237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vm3_21237/03_2026/6vm3_21237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vm3_21237/03_2026/6vm3_21237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vm3_21237/03_2026/6vm3_21237.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9900 2.51 5 N 2435 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15180 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "E" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "C" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "D" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.20 Number of scatterers: 15180 At special positions: 0 Unit cell: (95.76, 96.6, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2745 8.00 N 2435 7.00 C 9900 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 694.3 milliseconds 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 20 sheets defined 39.5% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.561A pdb=" N SER A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 Processing helix chain 'A' and resid 395 through 444 removed outlier: 3.814A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'E' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.562A pdb=" N SER E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 340 Processing helix chain 'E' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'C' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.561A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 340 Processing helix chain 'C' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.562A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 340 Processing helix chain 'B' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.573A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 265 removed outlier: 3.561A pdb=" N SER D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 340 Processing helix chain 'D' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 removed outlier: 8.069A pdb=" N CYS A 233 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG A 220 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 235 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP A 218 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG A 237 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 216 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS A 239 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 123 through 124 removed outlier: 8.070A pdb=" N CYS E 233 " --> pdb=" O ARG E 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG E 220 " --> pdb=" O CYS E 233 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU E 235 " --> pdb=" O ASP E 218 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP E 218 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG E 237 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU E 216 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS E 239 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 224 through 225 Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 123 through 124 removed outlier: 8.069A pdb=" N CYS C 233 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG C 220 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU C 235 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP C 218 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG C 237 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU C 216 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS C 239 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB4, first strand: chain 'B' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 123 through 124 removed outlier: 8.070A pdb=" N CYS B 233 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG B 220 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU B 235 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 218 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG B 237 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU B 216 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS B 239 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB8, first strand: chain 'D' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.581A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 removed outlier: 8.070A pdb=" N CYS D 233 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG D 220 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU D 235 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP D 218 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG D 237 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU D 216 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS D 239 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 865 hydrogen bonds defined for protein. 2550 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: 2.47 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2350 1.30 - 1.43: 4176 1.43 - 1.55: 8781 1.55 - 1.68: 87 1.68 - 1.81: 171 Bond restraints: 15565 Sorted by residual: bond pdb=" C43 IVM D 603 " pdb=" C44 IVM D 603 " ideal model delta sigma weight residual 1.330 1.682 -0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" C43 IVM E 901 " pdb=" C44 IVM E 901 " ideal model delta sigma weight residual 1.330 1.682 -0.352 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C43 IVM C 503 " pdb=" C44 IVM C 503 " ideal model delta sigma weight residual 1.330 1.681 -0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C43 IVM A 604 " pdb=" C44 IVM A 604 " ideal model delta sigma weight residual 1.330 1.681 -0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C43 IVM B 603 " pdb=" C44 IVM B 603 " ideal model delta sigma weight residual 1.330 1.681 -0.351 2.00e-02 2.50e+03 3.08e+02 ... (remaining 15560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.64: 20906 6.64 - 13.27: 159 13.27 - 19.91: 40 19.91 - 26.54: 5 26.54 - 33.18: 15 Bond angle restraints: 21125 Sorted by residual: angle pdb=" C7 IVM E 901 " pdb=" C6 IVM E 901 " pdb=" O14 IVM E 901 " ideal model delta sigma weight residual 106.56 73.38 33.18 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM C 503 " pdb=" C6 IVM C 503 " pdb=" O14 IVM C 503 " ideal model delta sigma weight residual 106.56 73.39 33.17 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM A 604 " pdb=" C6 IVM A 604 " pdb=" O14 IVM A 604 " ideal model delta sigma weight residual 106.56 73.39 33.17 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM B 603 " pdb=" C6 IVM B 603 " pdb=" O14 IVM B 603 " ideal model delta sigma weight residual 106.56 73.41 33.15 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM D 603 " pdb=" C6 IVM D 603 " pdb=" O14 IVM D 603 " ideal model delta sigma weight residual 106.56 73.43 33.13 3.00e+00 1.11e-01 1.22e+02 ... (remaining 21120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 8712 22.48 - 44.97: 818 44.97 - 67.45: 185 67.45 - 89.93: 110 89.93 - 112.42: 95 Dihedral angle restraints: 9920 sinusoidal: 4580 harmonic: 5340 Sorted by residual: dihedral pdb=" C25 IVM B 603 " pdb=" C26 IVM B 603 " pdb=" C27 IVM B 603 " pdb=" C29 IVM B 603 " ideal model delta sinusoidal sigma weight residual 51.04 -61.38 112.42 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C25 IVM E 901 " pdb=" C26 IVM E 901 " pdb=" C27 IVM E 901 " pdb=" C29 IVM E 901 " ideal model delta sinusoidal sigma weight residual 51.04 -61.32 112.36 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C25 IVM C 503 " pdb=" C26 IVM C 503 " pdb=" C27 IVM C 503 " pdb=" C29 IVM C 503 " ideal model delta sinusoidal sigma weight residual 51.04 -61.30 112.34 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 9917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2290 0.146 - 0.292: 105 0.292 - 0.439: 25 0.439 - 0.585: 5 0.585 - 0.731: 5 Chirality restraints: 2430 Sorted by residual: chirality pdb=" C6 IVM D 603 " pdb=" C11 IVM D 603 " pdb=" C7 IVM D 603 " pdb=" O14 IVM D 603 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C6 IVM A 604 " pdb=" C11 IVM A 604 " pdb=" C7 IVM A 604 " pdb=" O14 IVM A 604 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C6 IVM C 503 " pdb=" C11 IVM C 503 " pdb=" C7 IVM C 503 " pdb=" O14 IVM C 503 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 2427 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C37 IVM A 604 " 0.412 2.00e-02 2.50e+03 3.83e-01 1.83e+03 pdb=" C38 IVM A 604 " -0.436 2.00e-02 2.50e+03 pdb=" C39 IVM A 604 " -0.408 2.00e-02 2.50e+03 pdb=" C40 IVM A 604 " -0.020 2.00e-02 2.50e+03 pdb=" C47 IVM A 604 " 0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM D 603 " -0.412 2.00e-02 2.50e+03 3.82e-01 1.83e+03 pdb=" C38 IVM D 603 " 0.436 2.00e-02 2.50e+03 pdb=" C39 IVM D 603 " 0.408 2.00e-02 2.50e+03 pdb=" C40 IVM D 603 " 0.020 2.00e-02 2.50e+03 pdb=" C47 IVM D 603 " -0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM C 503 " -0.412 2.00e-02 2.50e+03 3.82e-01 1.83e+03 pdb=" C38 IVM C 503 " 0.436 2.00e-02 2.50e+03 pdb=" C39 IVM C 503 " 0.409 2.00e-02 2.50e+03 pdb=" C40 IVM C 503 " 0.019 2.00e-02 2.50e+03 pdb=" C47 IVM C 503 " -0.452 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3628 2.81 - 3.33: 14180 3.33 - 3.85: 25000 3.85 - 4.38: 28193 4.38 - 4.90: 50653 Nonbonded interactions: 121654 Sorted by model distance: nonbonded pdb=" OD1 ASN E 131 " pdb=" OG1 THR E 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN B 131 " pdb=" OG1 THR B 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN A 131 " pdb=" OG1 THR A 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN C 131 " pdb=" OG1 THR C 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN D 131 " pdb=" OG1 THR D 157 " model vdw 2.283 3.040 ... (remaining 121649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 444 or resid 604)) selection = (chain 'B' and (resid 32 through 444 or resid 603)) selection = chain 'C' selection = (chain 'D' and (resid 32 through 444 or resid 603)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.017 0.352 15570 Z= 0.782 Angle : 1.854 33.178 21140 Z= 0.816 Chirality : 0.090 0.731 2430 Planarity : 0.027 0.383 2590 Dihedral : 23.000 112.416 6450 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.92 % Allowed : 11.04 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1785 helix: 2.04 (0.18), residues: 680 sheet: 1.54 (0.26), residues: 415 loop : -1.25 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 83 TYR 0.032 0.005 TYR A 433 PHE 0.029 0.004 PHE E 169 TRP 0.015 0.003 TRP E 118 HIS 0.009 0.002 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.01683 (15565) covalent geometry : angle 1.85435 (21125) hydrogen bonds : bond 0.14680 ( 770) hydrogen bonds : angle 6.72208 ( 2550) link_BETA1-4 : bond 0.00140 ( 5) link_BETA1-4 : angle 1.84862 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8469 (mmt) cc_final: 0.8195 (mmt) REVERT: B 42 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8138 (mmt) REVERT: D 42 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8018 (mmt) outliers start: 15 outliers final: 8 residues processed: 160 average time/residue: 0.1222 time to fit residues: 29.5507 Evaluate side-chains 124 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 70 ASN A 133 HIS E 62 ASN E 70 ASN E 133 HIS C 62 ASN C 70 ASN C 133 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 70 ASN B 133 HIS D 62 ASN D 70 ASN D 133 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066024 restraints weight = 35134.078| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.18 r_work: 0.2850 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15570 Z= 0.146 Angle : 0.817 9.980 21140 Z= 0.372 Chirality : 0.050 0.303 2430 Planarity : 0.004 0.033 2590 Dihedral : 17.875 106.547 2880 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.60 % Allowed : 12.82 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1785 helix: 2.67 (0.18), residues: 730 sheet: 1.85 (0.26), residues: 410 loop : -1.27 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 237 TYR 0.025 0.002 TYR E 325 PHE 0.014 0.001 PHE C 422 TRP 0.007 0.001 TRP D 118 HIS 0.002 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00297 (15565) covalent geometry : angle 0.81099 (21125) hydrogen bonds : bond 0.05281 ( 770) hydrogen bonds : angle 4.94805 ( 2550) link_BETA1-4 : bond 0.00187 ( 5) link_BETA1-4 : angle 3.78241 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8875 (mmt) cc_final: 0.8596 (mmt) REVERT: E 113 MET cc_start: 0.8964 (ppp) cc_final: 0.8355 (ppp) REVERT: E 187 MET cc_start: 0.8797 (tpt) cc_final: 0.8449 (tpt) REVERT: C 80 MET cc_start: 0.8963 (mtt) cc_final: 0.8737 (mmm) REVERT: C 295 ARG cc_start: 0.8303 (mtp180) cc_final: 0.8001 (mtp180) REVERT: B 113 MET cc_start: 0.8914 (ppp) cc_final: 0.8155 (ppp) REVERT: B 154 ILE cc_start: 0.9081 (pt) cc_final: 0.8827 (tp) REVERT: D 113 MET cc_start: 0.9001 (ppp) cc_final: 0.8339 (ppp) REVERT: D 187 MET cc_start: 0.8805 (tpt) cc_final: 0.8563 (tpt) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.1383 time to fit residues: 31.3470 Evaluate side-chains 135 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.081656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062317 restraints weight = 36064.443| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.21 r_work: 0.2770 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15570 Z= 0.208 Angle : 0.758 10.640 21140 Z= 0.358 Chirality : 0.045 0.217 2430 Planarity : 0.004 0.028 2590 Dihedral : 13.629 88.047 2865 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.64 % Allowed : 13.07 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1785 helix: 3.03 (0.18), residues: 695 sheet: 1.97 (0.26), residues: 415 loop : -1.09 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 237 TYR 0.027 0.002 TYR E 325 PHE 0.013 0.002 PHE C 72 TRP 0.019 0.002 TRP D 263 HIS 0.004 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00476 (15565) covalent geometry : angle 0.74812 (21125) hydrogen bonds : bond 0.05438 ( 770) hydrogen bonds : angle 4.71025 ( 2550) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 4.70311 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8787 (p0) cc_final: 0.8572 (p0) REVERT: A 295 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7773 (mtm110) REVERT: E 187 MET cc_start: 0.8895 (tpt) cc_final: 0.8352 (tpt) REVERT: C 295 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7991 (mtp180) REVERT: B 113 MET cc_start: 0.8953 (ppp) cc_final: 0.8229 (ppp) REVERT: D 187 MET cc_start: 0.8820 (tpt) cc_final: 0.8517 (tpt) outliers start: 43 outliers final: 25 residues processed: 156 average time/residue: 0.1276 time to fit residues: 29.4421 Evaluate side-chains 142 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062324 restraints weight = 35681.592| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.19 r_work: 0.2764 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15570 Z= 0.190 Angle : 0.691 8.561 21140 Z= 0.334 Chirality : 0.045 0.235 2430 Planarity : 0.004 0.037 2590 Dihedral : 10.767 64.360 2865 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.76 % Allowed : 13.99 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1785 helix: 2.79 (0.18), residues: 730 sheet: 1.91 (0.26), residues: 415 loop : -1.07 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 333 TYR 0.026 0.002 TYR E 325 PHE 0.010 0.001 PHE E 72 TRP 0.011 0.002 TRP D 263 HIS 0.004 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00435 (15565) covalent geometry : angle 0.67600 (21125) hydrogen bonds : bond 0.05044 ( 770) hydrogen bonds : angle 4.60699 ( 2550) link_BETA1-4 : bond 0.00260 ( 5) link_BETA1-4 : angle 5.36161 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8081 (p0) REVERT: E 115 ASP cc_start: 0.8734 (p0) cc_final: 0.8505 (p0) REVERT: E 121 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8222 (p0) REVERT: E 187 MET cc_start: 0.8970 (tpt) cc_final: 0.8406 (tpt) REVERT: C 121 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8042 (p0) REVERT: C 295 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7928 (mtp180) REVERT: C 315 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (tt) REVERT: C 333 ARG cc_start: 0.7554 (mtp-110) cc_final: 0.7353 (mtm110) REVERT: B 113 MET cc_start: 0.8948 (ppp) cc_final: 0.8453 (ppp) REVERT: B 115 ASP cc_start: 0.8728 (p0) cc_final: 0.8494 (p0) REVERT: D 121 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8004 (p0) REVERT: D 187 MET cc_start: 0.8905 (tpt) cc_final: 0.8626 (tpt) outliers start: 45 outliers final: 28 residues processed: 152 average time/residue: 0.1142 time to fit residues: 26.9569 Evaluate side-chains 146 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.061952 restraints weight = 35727.496| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.17 r_work: 0.2762 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15570 Z= 0.187 Angle : 0.666 8.278 21140 Z= 0.324 Chirality : 0.044 0.210 2430 Planarity : 0.003 0.026 2590 Dihedral : 8.992 56.640 2865 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.31 % Allowed : 13.87 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.20), residues: 1785 helix: 3.11 (0.18), residues: 695 sheet: 1.89 (0.26), residues: 415 loop : -0.97 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.027 0.002 TYR E 325 PHE 0.011 0.001 PHE E 72 TRP 0.012 0.001 TRP D 263 HIS 0.003 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00427 (15565) covalent geometry : angle 0.65321 (21125) hydrogen bonds : bond 0.04933 ( 770) hydrogen bonds : angle 4.49970 ( 2550) link_BETA1-4 : bond 0.00132 ( 5) link_BETA1-4 : angle 4.90417 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8011 (p0) REVERT: E 121 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8214 (p0) REVERT: E 187 MET cc_start: 0.8992 (tpt) cc_final: 0.8766 (tpt) REVERT: C 121 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7968 (p0) REVERT: C 295 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7857 (mtp180) REVERT: C 315 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (tt) REVERT: C 333 ARG cc_start: 0.7512 (mtp-110) cc_final: 0.7289 (mtm110) REVERT: B 113 MET cc_start: 0.8930 (ppp) cc_final: 0.8522 (ppp) REVERT: B 315 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8656 (tt) REVERT: D 113 MET cc_start: 0.8903 (ppp) cc_final: 0.8159 (ppp) REVERT: D 121 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7983 (p0) REVERT: D 187 MET cc_start: 0.8930 (tpt) cc_final: 0.8658 (tpt) outliers start: 54 outliers final: 31 residues processed: 161 average time/residue: 0.1162 time to fit residues: 28.8785 Evaluate side-chains 155 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 121 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 109 optimal weight: 0.0570 chunk 134 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.063199 restraints weight = 35734.308| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.30 r_work: 0.2759 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15570 Z= 0.164 Angle : 0.636 7.868 21140 Z= 0.310 Chirality : 0.042 0.185 2430 Planarity : 0.003 0.026 2590 Dihedral : 8.191 56.396 2865 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.25 % Allowed : 14.54 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1785 helix: 3.17 (0.18), residues: 695 sheet: 1.81 (0.26), residues: 415 loop : -0.98 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.026 0.002 TYR E 325 PHE 0.010 0.001 PHE A 425 TRP 0.013 0.001 TRP B 263 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00373 (15565) covalent geometry : angle 0.62476 (21125) hydrogen bonds : bond 0.04696 ( 770) hydrogen bonds : angle 4.37101 ( 2550) link_BETA1-4 : bond 0.00298 ( 5) link_BETA1-4 : angle 4.58409 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7981 (p0) REVERT: A 295 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8119 (mtp180) REVERT: E 113 MET cc_start: 0.8789 (ppp) cc_final: 0.7876 (ppp) REVERT: E 121 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8194 (p0) REVERT: E 187 MET cc_start: 0.9039 (tpt) cc_final: 0.8827 (tpt) REVERT: C 107 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9008 (tt) REVERT: C 121 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7918 (p0) REVERT: C 189 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8555 (t0) REVERT: C 295 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7930 (mtp180) REVERT: C 315 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8629 (tt) REVERT: C 333 ARG cc_start: 0.7546 (mtp-110) cc_final: 0.7330 (mtm110) REVERT: D 121 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7948 (p0) REVERT: D 187 MET cc_start: 0.8964 (tpt) cc_final: 0.8707 (tpt) outliers start: 53 outliers final: 32 residues processed: 165 average time/residue: 0.1288 time to fit residues: 31.5378 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.064602 restraints weight = 35348.350| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.15 r_work: 0.2834 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15570 Z= 0.121 Angle : 0.616 10.677 21140 Z= 0.298 Chirality : 0.041 0.154 2430 Planarity : 0.003 0.038 2590 Dihedral : 7.653 56.643 2865 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.01 % Allowed : 14.60 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1785 helix: 3.24 (0.18), residues: 695 sheet: 1.81 (0.26), residues: 415 loop : -0.99 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.023 0.002 TYR E 325 PHE 0.010 0.001 PHE C 425 TRP 0.016 0.001 TRP B 263 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00261 (15565) covalent geometry : angle 0.60546 (21125) hydrogen bonds : bond 0.04239 ( 770) hydrogen bonds : angle 4.13120 ( 2550) link_BETA1-4 : bond 0.00291 ( 5) link_BETA1-4 : angle 4.32817 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.602 Fit side-chains REVERT: A 113 MET cc_start: 0.8846 (ppp) cc_final: 0.8603 (ppp) REVERT: A 121 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7960 (p0) REVERT: A 189 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8290 (t0) REVERT: A 295 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8131 (mtp180) REVERT: E 121 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8160 (p0) REVERT: C 121 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7912 (p0) REVERT: C 295 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8137 (mtm110) REVERT: C 311 MET cc_start: 0.8997 (mmt) cc_final: 0.8683 (mmt) REVERT: C 333 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7322 (mtm110) REVERT: B 107 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 113 MET cc_start: 0.8817 (ppp) cc_final: 0.8004 (ppp) REVERT: B 187 MET cc_start: 0.9104 (tpt) cc_final: 0.8669 (tpt) REVERT: D 121 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7948 (p0) outliers start: 49 outliers final: 32 residues processed: 166 average time/residue: 0.1244 time to fit residues: 30.9615 Evaluate side-chains 166 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.061198 restraints weight = 36161.992| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.17 r_work: 0.2753 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15570 Z= 0.253 Angle : 0.679 10.481 21140 Z= 0.339 Chirality : 0.043 0.149 2430 Planarity : 0.005 0.143 2590 Dihedral : 7.662 56.177 2865 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.87 % Allowed : 14.23 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1785 helix: 3.04 (0.18), residues: 695 sheet: 1.94 (0.27), residues: 390 loop : -1.07 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 333 TYR 0.028 0.002 TYR E 325 PHE 0.014 0.002 PHE C 72 TRP 0.020 0.002 TRP D 263 HIS 0.003 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00588 (15565) covalent geometry : angle 0.66979 (21125) hydrogen bonds : bond 0.05208 ( 770) hydrogen bonds : angle 4.54071 ( 2550) link_BETA1-4 : bond 0.00177 ( 5) link_BETA1-4 : angle 4.25977 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 0.592 Fit side-chains REVERT: A 121 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8079 (p0) REVERT: A 189 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8134 (t0) REVERT: E 113 MET cc_start: 0.8759 (ppp) cc_final: 0.7973 (ppp) REVERT: E 121 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (p0) REVERT: E 187 MET cc_start: 0.8984 (tpt) cc_final: 0.8673 (tpt) REVERT: C 107 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9117 (tt) REVERT: C 121 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8016 (p0) REVERT: C 315 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8836 (tt) REVERT: C 333 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7446 (mtm110) REVERT: B 107 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9066 (tt) REVERT: B 187 MET cc_start: 0.9104 (tpt) cc_final: 0.8693 (tpt) REVERT: D 113 MET cc_start: 0.8794 (ppp) cc_final: 0.8326 (ppp) REVERT: D 121 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8056 (p0) REVERT: D 187 MET cc_start: 0.9070 (tpt) cc_final: 0.8689 (tpt) outliers start: 63 outliers final: 38 residues processed: 171 average time/residue: 0.1208 time to fit residues: 31.3929 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 161 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.083925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.064406 restraints weight = 35600.340| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.17 r_work: 0.2834 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15570 Z= 0.119 Angle : 0.624 10.441 21140 Z= 0.302 Chirality : 0.041 0.129 2430 Planarity : 0.004 0.071 2590 Dihedral : 7.264 55.584 2865 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.19 % Allowed : 14.72 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1785 helix: 3.20 (0.18), residues: 695 sheet: 1.87 (0.26), residues: 390 loop : -1.08 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 333 TYR 0.023 0.002 TYR E 325 PHE 0.012 0.001 PHE D 422 TRP 0.016 0.001 TRP B 263 HIS 0.002 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00252 (15565) covalent geometry : angle 0.61537 (21125) hydrogen bonds : bond 0.04221 ( 770) hydrogen bonds : angle 4.12818 ( 2550) link_BETA1-4 : bond 0.00301 ( 5) link_BETA1-4 : angle 3.93676 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.489 Fit side-chains REVERT: A 121 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7929 (p0) REVERT: A 189 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 295 ARG cc_start: 0.8436 (mtp180) cc_final: 0.8174 (mtm110) REVERT: E 113 MET cc_start: 0.8649 (ppp) cc_final: 0.7974 (ppp) REVERT: E 121 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8157 (p0) REVERT: E 187 MET cc_start: 0.9019 (tpt) cc_final: 0.8646 (tpt) REVERT: C 107 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9083 (tt) REVERT: C 121 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7889 (p0) REVERT: C 333 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7366 (mtm110) REVERT: B 107 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9031 (tt) REVERT: B 113 MET cc_start: 0.8545 (ppp) cc_final: 0.7774 (ppp) REVERT: B 187 MET cc_start: 0.9167 (tpt) cc_final: 0.8772 (tpt) REVERT: B 189 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8112 (t0) REVERT: D 113 MET cc_start: 0.8662 (ppp) cc_final: 0.7691 (ppp) REVERT: D 115 ASP cc_start: 0.8755 (p0) cc_final: 0.8503 (m-30) REVERT: D 121 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8061 (p0) REVERT: D 187 MET cc_start: 0.9065 (tpt) cc_final: 0.8672 (tpt) REVERT: D 311 MET cc_start: 0.8942 (mmp) cc_final: 0.8568 (mmt) outliers start: 52 outliers final: 33 residues processed: 171 average time/residue: 0.1110 time to fit residues: 29.0757 Evaluate side-chains 167 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064583 restraints weight = 35725.575| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.17 r_work: 0.2831 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15570 Z= 0.124 Angle : 0.624 12.225 21140 Z= 0.302 Chirality : 0.041 0.127 2430 Planarity : 0.003 0.049 2590 Dihedral : 6.997 57.046 2865 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.58 % Allowed : 15.40 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1785 helix: 3.16 (0.18), residues: 695 sheet: 1.85 (0.27), residues: 390 loop : -1.07 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 333 TYR 0.023 0.002 TYR C 325 PHE 0.009 0.001 PHE A 425 TRP 0.017 0.001 TRP D 263 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00270 (15565) covalent geometry : angle 0.61634 (21125) hydrogen bonds : bond 0.04155 ( 770) hydrogen bonds : angle 4.05385 ( 2550) link_BETA1-4 : bond 0.00232 ( 5) link_BETA1-4 : angle 3.74769 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.620 Fit side-chains REVERT: A 121 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 189 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8294 (t0) REVERT: A 295 ARG cc_start: 0.8435 (mtp180) cc_final: 0.8143 (mtm110) REVERT: E 121 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8097 (p0) REVERT: E 187 MET cc_start: 0.9035 (tpt) cc_final: 0.8679 (tpt) REVERT: E 189 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8093 (t0) REVERT: C 107 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9075 (tt) REVERT: C 113 MET cc_start: 0.8202 (ppp) cc_final: 0.7644 (ppp) REVERT: C 121 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7816 (p0) REVERT: C 333 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7351 (mtm110) REVERT: B 107 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9006 (tt) REVERT: B 187 MET cc_start: 0.9160 (tpt) cc_final: 0.8763 (tpt) REVERT: B 189 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8092 (t0) REVERT: D 113 MET cc_start: 0.8740 (ppp) cc_final: 0.8288 (ppp) REVERT: D 121 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7997 (p0) REVERT: D 187 MET cc_start: 0.9066 (tpt) cc_final: 0.8696 (tpt) outliers start: 42 outliers final: 32 residues processed: 163 average time/residue: 0.1071 time to fit residues: 27.3698 Evaluate side-chains 167 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065577 restraints weight = 35643.408| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.16 r_work: 0.2853 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15570 Z= 0.115 Angle : 0.617 13.826 21140 Z= 0.296 Chirality : 0.040 0.199 2430 Planarity : 0.004 0.048 2590 Dihedral : 6.690 56.080 2865 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.94 % Allowed : 15.15 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1785 helix: 3.20 (0.18), residues: 695 sheet: 1.79 (0.27), residues: 390 loop : -1.08 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 333 TYR 0.021 0.002 TYR C 325 PHE 0.009 0.001 PHE C 425 TRP 0.016 0.001 TRP D 263 HIS 0.002 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00249 (15565) covalent geometry : angle 0.60997 (21125) hydrogen bonds : bond 0.03922 ( 770) hydrogen bonds : angle 3.89068 ( 2550) link_BETA1-4 : bond 0.00223 ( 5) link_BETA1-4 : angle 3.41605 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.81 seconds wall clock time: 50 minutes 1.58 seconds (3001.58 seconds total)