Starting phenix.real_space_refine on Tue Jul 29 14:52:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm2_50547/07_2025/9fm2_50547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm2_50547/07_2025/9fm2_50547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fm2_50547/07_2025/9fm2_50547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm2_50547/07_2025/9fm2_50547.map" model { file = "/net/cci-nas-00/data/ceres_data/9fm2_50547/07_2025/9fm2_50547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm2_50547/07_2025/9fm2_50547.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 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 116 5.16 5 C 7260 2.51 5 N 2005 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11567 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain breaks: 2 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 331} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2674 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 331} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 331} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.23, per 1000 atoms: 0.63 Number of scatterers: 11567 At special positions: 0 Unit cell: (115.2, 115.2, 92.16, 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 116 16.00 O 2186 8.00 N 2005 7.00 C 7260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.06 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.06 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.05 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.08 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.10 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.00 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.06 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=1.97 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.07 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.00 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.00 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.05 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.05 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.04 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.00 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 420 " distance=2.05 Simple disulfide: pdb=" SG CYS E 122 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 229 " distance=1.99 Simple disulfide: pdb=" SG CYS E 231 " - pdb=" SG CYS E 236 " distance=2.08 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.04 Simple disulfide: pdb=" SG CYS E 424 " - pdb=" SG CYS E 447 " distance=1.99 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 NAG-ASN " NAG B 500 " - " ASN B 284 " " NAG C 500 " - " ASN C 284 " " NAG D 500 " - " ASN D 284 " " NAG E 500 " - " ASN E 284 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 30 sheets defined 1.2% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.721A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.504A pdb=" N THR A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 196 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.937A pdb=" N THR A 68 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.620A pdb=" N LEU A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 38 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 89 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 98 removed outlier: 6.930A pdb=" N ILE B 445 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 97 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 443 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 122 removed outlier: 5.840A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 121 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 128 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 131 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 155 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET B 174 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER B 158 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 172 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 179 through 183 removed outlier: 4.324A pdb=" N ASP B 212 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 206 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.739A pdb=" N ASN B 230 " --> pdb=" O TYR B 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.593A pdb=" N GLU B 250 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 253 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 264 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS B 255 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 269 removed outlier: 3.510A pdb=" N ILE B 314 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR B 278 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 292 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 352 through 356 removed outlier: 3.618A pdb=" N VAL B 353 " --> pdb=" O TRP B 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 380 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.137A pdb=" N LYS C 94 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N CYS C 447 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 448 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 411 " --> pdb=" O GLY C 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 115 through 122 removed outlier: 5.795A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 121 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 131 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET C 174 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER C 158 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 172 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 180 through 183 removed outlier: 4.540A pdb=" N ASP C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 206 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR C 210 " --> pdb=" O TYR C 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG C 223 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 230 " --> pdb=" O TYR C 237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG C 223 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 238 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 254 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE C 253 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU C 264 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS C 255 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.536A pdb=" N ILE C 314 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 311 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 303 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG C 292 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU C 276 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 98 removed outlier: 6.976A pdb=" N ILE D 445 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU D 97 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR D 443 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 122 removed outlier: 5.655A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 121 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 131 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU D 156 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 171 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 179 through 183 removed outlier: 4.458A pdb=" N ASP D 212 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR D 206 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.626A pdb=" N ASN D 230 " --> pdb=" O TYR D 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.510A pdb=" N PHE D 253 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU D 264 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 255 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 268 through 269 removed outlier: 3.538A pdb=" N ILE D 314 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 303 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG D 292 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU D 276 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 352 through 356 removed outlier: 3.546A pdb=" N TYR D 380 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 367 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N MET D 377 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL D 399 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU D 379 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 92 through 98 removed outlier: 6.853A pdb=" N ILE E 445 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 97 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR E 443 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 448 " --> pdb=" O PRO E 423 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 115 through 122 removed outlier: 5.744A pdb=" N GLU E 117 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU E 132 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 121 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 128 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 159 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 131 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E 157 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 180 through 183 removed outlier: 3.525A pdb=" N TYR E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP E 212 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR E 206 " --> pdb=" O TYR E 210 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR E 210 " --> pdb=" O TYR E 206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG E 223 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN E 230 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG E 223 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE E 253 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU E 264 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS E 255 " --> pdb=" O ILE E 262 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 268 through 269 removed outlier: 3.884A pdb=" N THR E 311 " --> pdb=" O ASN E 306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 303 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG E 292 " --> pdb=" O GLU E 276 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU E 276 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 352 through 356 removed outlier: 3.516A pdb=" N GLY E 362 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET E 377 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL E 399 " --> pdb=" O MET E 377 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU E 379 " --> pdb=" O SER E 397 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 882 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: 4.10 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1927 1.31 - 1.45: 3340 1.45 - 1.58: 6398 1.58 - 1.71: 2 1.71 - 1.84: 162 Bond restraints: 11829 Sorted by residual: bond pdb=" C PRO D 423 " pdb=" O PRO D 423 " ideal model delta sigma weight residual 1.235 1.190 0.045 7.90e-03 1.60e+04 3.31e+01 bond pdb=" C PRO E 423 " pdb=" O PRO E 423 " ideal model delta sigma weight residual 1.235 1.195 0.040 7.90e-03 1.60e+04 2.53e+01 bond pdb=" C ILE D 191 " pdb=" O ILE D 191 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.01e-02 9.80e+03 1.97e+01 bond pdb=" C ILE B 191 " pdb=" O ILE B 191 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.01e-02 9.80e+03 1.85e+01 bond pdb=" C ARG B 363 " pdb=" O ARG B 363 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.14e-02 7.69e+03 1.66e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14724 1.95 - 3.89: 1078 3.89 - 5.84: 147 5.84 - 7.78: 20 7.78 - 9.73: 6 Bond angle restraints: 15975 Sorted by residual: angle pdb=" N CYS B 277 " pdb=" CA CYS B 277 " pdb=" C CYS B 277 " ideal model delta sigma weight residual 108.75 118.45 -9.70 1.71e+00 3.42e-01 3.22e+01 angle pdb=" CG MET C 449 " pdb=" SD MET C 449 " pdb=" CE MET C 449 " ideal model delta sigma weight residual 100.90 110.63 -9.73 2.20e+00 2.07e-01 1.95e+01 angle pdb=" CA ASP D 197 " pdb=" CB ASP D 197 " pdb=" CG ASP D 197 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CA CYS C 229 " pdb=" CB CYS C 229 " pdb=" SG CYS C 229 " ideal model delta sigma weight residual 114.40 123.39 -8.99 2.30e+00 1.89e-01 1.53e+01 angle pdb=" CA CYS D 229 " pdb=" CB CYS D 229 " pdb=" SG CYS D 229 " ideal model delta sigma weight residual 114.40 123.17 -8.77 2.30e+00 1.89e-01 1.45e+01 ... (remaining 15970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 6440 16.81 - 33.61: 576 33.61 - 50.42: 106 50.42 - 67.22: 25 67.22 - 84.03: 7 Dihedral angle restraints: 7154 sinusoidal: 2919 harmonic: 4235 Sorted by residual: dihedral pdb=" CB CYS B 277 " pdb=" SG CYS B 277 " pdb=" SG CYS B 291 " pdb=" CB CYS B 291 " ideal model delta sinusoidal sigma weight residual 93.00 48.89 44.11 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS E 318 " pdb=" SG CYS E 318 " pdb=" SG CYS E 337 " pdb=" CB CYS E 337 " ideal model delta sinusoidal sigma weight residual 93.00 129.87 -36.87 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA ALA C 290 " pdb=" C ALA C 290 " pdb=" N CYS C 291 " pdb=" CA CYS C 291 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 994 0.062 - 0.124: 534 0.124 - 0.186: 150 0.186 - 0.248: 41 0.248 - 0.310: 7 Chirality restraints: 1726 Sorted by residual: chirality pdb=" C1 NAG E 500 " pdb=" ND2 ASN E 284 " pdb=" C2 NAG E 500 " pdb=" O5 NAG E 500 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG C 500 " pdb=" ND2 ASN C 284 " pdb=" C2 NAG C 500 " pdb=" O5 NAG C 500 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLU E 258 " pdb=" N GLU E 258 " pdb=" C GLU E 258 " pdb=" CB GLU E 258 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1723 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 446 " 0.055 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR C 446 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR C 446 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 446 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR C 446 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR C 446 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR C 446 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR C 446 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 177 " 0.023 2.00e-02 2.50e+03 3.20e-02 2.56e+01 pdb=" CG TRP D 177 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP D 177 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP D 177 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP D 177 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 177 " -0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP D 177 " -0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 177 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 177 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP D 177 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 210 " -0.018 2.00e-02 2.50e+03 2.93e-02 1.72e+01 pdb=" CG TYR B 210 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 210 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 210 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 210 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 210 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 210 " 0.035 2.00e-02 2.50e+03 pdb=" OH TYR B 210 " -0.041 2.00e-02 2.50e+03 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3004 2.81 - 3.33: 9590 3.33 - 3.85: 18820 3.85 - 4.38: 21225 4.38 - 4.90: 37276 Nonbonded interactions: 89915 Sorted by model distance: nonbonded pdb=" OD2 ASP A 52 " pdb=" OG SER A 56 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR D 278 " pdb=" NZ LYS D 349 " model vdw 2.290 3.120 nonbonded pdb=" OD1 ASP B 194 " pdb=" NZ LYS B 203 " model vdw 2.291 3.120 nonbonded pdb=" OD2 ASP E 194 " pdb=" NZ LYS E 203 " model vdw 2.292 3.120 nonbonded pdb=" OG1 THR E 319 " pdb=" O ASP E 392 " model vdw 2.297 3.040 ... (remaining 89910 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 'B' and (resid 79 through 134 or resid 151 through 455 or resid 500)) selection = chain 'C' selection = (chain 'D' and (resid 79 through 134 or resid 151 through 455 or resid 500)) selection = (chain 'E' and (resid 79 through 134 or resid 151 through 455 or resid 500)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.430 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.010 0.078 11866 Z= 0.627 Angle : 1.155 9.726 16053 Z= 0.678 Chirality : 0.080 0.310 1726 Planarity : 0.008 0.101 2046 Dihedral : 13.319 84.028 4357 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.20), residues: 1454 helix: None (None), residues: 0 sheet: -0.57 (0.22), residues: 535 loop : -1.55 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.010 TRP D 177 HIS 0.022 0.005 HIS C 129 PHE 0.057 0.009 PHE B 172 TYR 0.055 0.008 TYR C 446 ARG 0.017 0.002 ARG D 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 0.84110 ( 12) hydrogen bonds : bond 0.30513 ( 324) hydrogen bonds : angle 10.97479 ( 882) SS BOND : bond 0.02875 ( 33) SS BOND : angle 1.80835 ( 66) covalent geometry : bond 0.01014 (11829) covalent geometry : angle 1.15149 (15975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.4263 (tt) cc_final: 0.3866 (tp) REVERT: A 64 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7745 (mmmt) REVERT: A 66 ARG cc_start: 0.7424 (ttp80) cc_final: 0.6769 (tpt90) REVERT: A 82 MET cc_start: 0.7236 (mpp) cc_final: 0.6857 (mmt) REVERT: A 90 TYR cc_start: 0.8379 (m-80) cc_final: 0.8088 (m-80) REVERT: B 206 TYR cc_start: 0.9175 (t80) cc_final: 0.8095 (t80) REVERT: B 357 MET cc_start: 0.8421 (mpp) cc_final: 0.7982 (mpp) REVERT: C 220 ASN cc_start: 0.8316 (t0) cc_final: 0.7920 (t0) REVERT: C 239 MET cc_start: 0.7504 (ttp) cc_final: 0.6930 (ttp) REVERT: C 337 CYS cc_start: 0.8542 (m) cc_final: 0.7907 (t) REVERT: C 427 ILE cc_start: 0.8991 (mt) cc_final: 0.8787 (mt) REVERT: C 449 MET cc_start: 0.7107 (mtm) cc_final: 0.6521 (mtm) REVERT: D 119 PHE cc_start: 0.6797 (p90) cc_final: 0.6400 (p90) REVERT: D 208 GLU cc_start: 0.8758 (mp0) cc_final: 0.8384 (tp30) REVERT: D 222 LEU cc_start: 0.8426 (tp) cc_final: 0.8169 (tp) REVERT: D 239 MET cc_start: 0.6508 (ttp) cc_final: 0.6260 (ttp) REVERT: D 305 LEU cc_start: 0.6658 (tt) cc_final: 0.6356 (tt) REVERT: D 357 MET cc_start: 0.7562 (mpp) cc_final: 0.7069 (mpp) REVERT: D 429 MET cc_start: 0.7076 (mtt) cc_final: 0.6707 (mtt) REVERT: D 449 MET cc_start: 0.7122 (ttm) cc_final: 0.6898 (ttm) REVERT: D 453 GLN cc_start: 0.8365 (pp30) cc_final: 0.8127 (pp30) REVERT: E 168 GLU cc_start: 0.5420 (tt0) cc_final: 0.4861 (tt0) REVERT: E 239 MET cc_start: 0.4977 (ttm) cc_final: 0.4217 (ttm) REVERT: E 254 LEU cc_start: 0.7145 (mm) cc_final: 0.6876 (mm) REVERT: E 285 LYS cc_start: 0.7806 (mppt) cc_final: 0.7372 (tttp) REVERT: E 305 LEU cc_start: 0.7958 (tt) cc_final: 0.7682 (tt) REVERT: E 403 MET cc_start: 0.9183 (mpp) cc_final: 0.8965 (mtt) REVERT: E 449 MET cc_start: 0.7576 (mtm) cc_final: 0.7114 (mtm) REVERT: E 453 GLN cc_start: 0.8360 (pp30) cc_final: 0.7856 (pp30) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2528 time to fit residues: 81.3770 Evaluate side-chains 163 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 169 ASN C 199 ASN D 306 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.176581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.140405 restraints weight = 18289.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.145336 restraints weight = 10374.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.148720 restraints weight = 7466.845| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11866 Z= 0.141 Angle : 0.641 9.182 16053 Z= 0.331 Chirality : 0.046 0.161 1726 Planarity : 0.004 0.045 2046 Dihedral : 6.061 54.038 1700 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.05 % Allowed : 8.27 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.33 (0.21), residues: 599 loop : -1.31 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 36 HIS 0.007 0.001 HIS B 101 PHE 0.014 0.001 PHE B 281 TYR 0.017 0.002 TYR E 365 ARG 0.008 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 4) link_NAG-ASN : angle 0.90313 ( 12) hydrogen bonds : bond 0.04556 ( 324) hydrogen bonds : angle 7.56505 ( 882) SS BOND : bond 0.00492 ( 33) SS BOND : angle 1.21620 ( 66) covalent geometry : bond 0.00303 (11829) covalent geometry : angle 0.63725 (15975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6884 (mpp) cc_final: 0.6340 (mmp) REVERT: B 97 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7461 (pp) REVERT: C 225 GLN cc_start: 0.7974 (mp10) cc_final: 0.7483 (mp10) REVERT: C 239 MET cc_start: 0.4474 (ttp) cc_final: 0.4193 (ttp) REVERT: C 287 ILE cc_start: 0.8876 (mt) cc_final: 0.8591 (mm) REVERT: C 369 MET cc_start: 0.5015 (mtp) cc_final: 0.4801 (mtp) REVERT: C 409 TYR cc_start: 0.7164 (m-80) cc_final: 0.6769 (m-80) REVERT: D 197 ASP cc_start: 0.7767 (p0) cc_final: 0.7505 (t70) REVERT: D 239 MET cc_start: 0.5249 (ttp) cc_final: 0.4821 (ttp) REVERT: D 292 ARG cc_start: 0.7466 (ttt180) cc_final: 0.7204 (tmm-80) REVERT: D 429 MET cc_start: 0.7420 (mtt) cc_final: 0.6820 (mtt) REVERT: E 453 GLN cc_start: 0.7648 (pp30) cc_final: 0.7265 (pp30) outliers start: 13 outliers final: 10 residues processed: 192 average time/residue: 0.2518 time to fit residues: 70.7385 Evaluate side-chains 175 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 409 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 52 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN E 230 ASN E 306 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.169072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.131964 restraints weight = 19130.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.136567 restraints weight = 11183.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.139599 restraints weight = 8200.615| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11866 Z= 0.292 Angle : 0.770 11.985 16053 Z= 0.398 Chirality : 0.050 0.241 1726 Planarity : 0.005 0.037 2046 Dihedral : 6.406 57.756 1700 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.00 % Allowed : 12.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1454 helix: None (None), residues: 0 sheet: -0.38 (0.22), residues: 575 loop : -1.61 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 177 HIS 0.008 0.002 HIS E 155 PHE 0.023 0.002 PHE D 119 TYR 0.024 0.002 TYR E 365 ARG 0.006 0.001 ARG D 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 1.01830 ( 12) hydrogen bonds : bond 0.05263 ( 324) hydrogen bonds : angle 7.46107 ( 882) SS BOND : bond 0.00713 ( 33) SS BOND : angle 1.83237 ( 66) covalent geometry : bond 0.00681 (11829) covalent geometry : angle 0.76244 (15975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7477 (m-30) cc_final: 0.7137 (m-30) REVERT: B 227 SER cc_start: 0.8461 (t) cc_final: 0.8065 (m) REVERT: C 287 ILE cc_start: 0.9046 (mt) cc_final: 0.8753 (mm) REVERT: C 375 MET cc_start: 0.7276 (tpp) cc_final: 0.6564 (tmm) REVERT: D 197 ASP cc_start: 0.7768 (p0) cc_final: 0.7482 (t70) REVERT: D 203 LYS cc_start: 0.8214 (pttm) cc_final: 0.7753 (ptpt) REVERT: D 221 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7810 (mm) REVERT: D 225 GLN cc_start: 0.7730 (mp10) cc_final: 0.7106 (mp10) REVERT: D 285 LYS cc_start: 0.7926 (tptt) cc_final: 0.7270 (tppt) REVERT: D 375 MET cc_start: 0.6194 (tmm) cc_final: 0.5986 (ppp) REVERT: D 429 MET cc_start: 0.7340 (mtt) cc_final: 0.6781 (mtt) REVERT: E 404 LYS cc_start: 0.8375 (pttt) cc_final: 0.7804 (pttm) REVERT: E 453 GLN cc_start: 0.7834 (pp30) cc_final: 0.7446 (pp30) outliers start: 37 outliers final: 24 residues processed: 185 average time/residue: 0.2292 time to fit residues: 61.5057 Evaluate side-chains 176 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 29 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 169 ASN C 169 ASN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.168842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.132637 restraints weight = 18887.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.137241 restraints weight = 11017.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.140192 restraints weight = 8053.255| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11866 Z= 0.225 Angle : 0.703 10.682 16053 Z= 0.363 Chirality : 0.048 0.167 1726 Planarity : 0.004 0.039 2046 Dihedral : 6.311 58.301 1700 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.40 % Allowed : 13.86 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.41 (0.21), residues: 598 loop : -1.53 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 177 HIS 0.006 0.001 HIS D 155 PHE 0.020 0.002 PHE D 119 TYR 0.019 0.002 TYR E 365 ARG 0.004 0.001 ARG B 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 1.09275 ( 12) hydrogen bonds : bond 0.04572 ( 324) hydrogen bonds : angle 7.22554 ( 882) SS BOND : bond 0.00665 ( 33) SS BOND : angle 1.74424 ( 66) covalent geometry : bond 0.00521 (11829) covalent geometry : angle 0.69517 (15975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8499 (mm) cc_final: 0.8072 (tp) REVERT: A 75 LYS cc_start: 0.8420 (pptt) cc_final: 0.8164 (pttp) REVERT: B 171 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8125 (pt) REVERT: B 201 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7052 (tt) REVERT: B 206 TYR cc_start: 0.8548 (t80) cc_final: 0.7668 (t80) REVERT: B 227 SER cc_start: 0.8469 (t) cc_final: 0.8082 (m) REVERT: C 225 GLN cc_start: 0.8484 (mp10) cc_final: 0.8211 (mp10) REVERT: C 287 ILE cc_start: 0.9026 (mt) cc_final: 0.8745 (mm) REVERT: D 197 ASP cc_start: 0.7725 (p0) cc_final: 0.7129 (t0) REVERT: D 203 LYS cc_start: 0.8238 (pttm) cc_final: 0.7756 (ptpt) REVERT: D 239 MET cc_start: 0.6620 (ttp) cc_final: 0.6258 (ttp) REVERT: D 429 MET cc_start: 0.7313 (mtt) cc_final: 0.6779 (mtt) REVERT: D 454 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7352 (tp) REVERT: E 287 ILE cc_start: 0.8895 (tt) cc_final: 0.8682 (pt) REVERT: E 305 LEU cc_start: 0.7747 (tt) cc_final: 0.7370 (tp) REVERT: E 404 LYS cc_start: 0.8376 (pttt) cc_final: 0.7806 (pttm) REVERT: E 453 GLN cc_start: 0.7778 (pp30) cc_final: 0.7566 (pp30) outliers start: 42 outliers final: 25 residues processed: 188 average time/residue: 0.2210 time to fit residues: 61.2773 Evaluate side-chains 180 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** D 230 ASN ** 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 = 0.4449 r_free = 0.4449 target = 0.168550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.131800 restraints weight = 18925.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.136272 restraints weight = 11240.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.139242 restraints weight = 8309.882| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11866 Z= 0.236 Angle : 0.729 11.305 16053 Z= 0.374 Chirality : 0.048 0.214 1726 Planarity : 0.004 0.042 2046 Dihedral : 6.309 56.320 1700 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.65 % Allowed : 15.40 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.48 (0.21), residues: 592 loop : -1.63 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 177 HIS 0.006 0.001 HIS B 129 PHE 0.016 0.002 PHE B 130 TYR 0.018 0.002 TYR E 365 ARG 0.006 0.001 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 1.18998 ( 12) hydrogen bonds : bond 0.04579 ( 324) hydrogen bonds : angle 7.14795 ( 882) SS BOND : bond 0.00699 ( 33) SS BOND : angle 2.03739 ( 66) covalent geometry : bond 0.00551 (11829) covalent geometry : angle 0.71860 (15975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8541 (mm) cc_final: 0.8094 (tt) REVERT: A 37 TYR cc_start: 0.8051 (m-10) cc_final: 0.7829 (m-10) REVERT: A 75 LYS cc_start: 0.8606 (pptt) cc_final: 0.8381 (pttp) REVERT: B 97 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7826 (pp) REVERT: B 171 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8149 (pt) REVERT: B 201 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6942 (tt) REVERT: B 206 TYR cc_start: 0.8588 (t80) cc_final: 0.7573 (t80) REVERT: B 227 SER cc_start: 0.8436 (t) cc_final: 0.8082 (m) REVERT: C 239 MET cc_start: 0.4382 (ttm) cc_final: 0.3786 (ttm) REVERT: C 287 ILE cc_start: 0.8977 (mt) cc_final: 0.8698 (mm) REVERT: D 197 ASP cc_start: 0.7639 (p0) cc_final: 0.7219 (t0) REVERT: D 203 LYS cc_start: 0.8296 (pttm) cc_final: 0.7860 (ptpt) REVERT: D 285 LYS cc_start: 0.8004 (tptt) cc_final: 0.7429 (tppt) REVERT: D 403 MET cc_start: 0.7827 (tpp) cc_final: 0.7564 (tpp) REVERT: D 429 MET cc_start: 0.7422 (mtt) cc_final: 0.6950 (mtt) REVERT: E 201 LEU cc_start: 0.7886 (pt) cc_final: 0.7542 (pp) REVERT: E 305 LEU cc_start: 0.7800 (tt) cc_final: 0.7475 (tp) REVERT: E 404 LYS cc_start: 0.8500 (pttt) cc_final: 0.7921 (pttm) REVERT: E 453 GLN cc_start: 0.7861 (pp30) cc_final: 0.7612 (pp30) outliers start: 45 outliers final: 32 residues processed: 181 average time/residue: 0.2805 time to fit residues: 78.1492 Evaluate side-chains 183 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 210 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 26 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 0.0870 chunk 138 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 136 optimal weight: 0.0010 overall best weight: 1.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS D 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.172081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.135803 restraints weight = 18919.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.140606 restraints weight = 10848.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.143629 restraints weight = 7845.594| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 11866 Z= 0.131 Angle : 0.643 10.169 16053 Z= 0.326 Chirality : 0.045 0.246 1726 Planarity : 0.004 0.040 2046 Dihedral : 5.980 55.439 1700 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.57 % Allowed : 16.05 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.21 (0.22), residues: 573 loop : -1.55 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.009 0.001 HIS B 101 PHE 0.011 0.001 PHE B 130 TYR 0.014 0.001 TYR E 365 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 4) link_NAG-ASN : angle 1.04314 ( 12) hydrogen bonds : bond 0.03837 ( 324) hydrogen bonds : angle 6.69005 ( 882) SS BOND : bond 0.00612 ( 33) SS BOND : angle 1.73105 ( 66) covalent geometry : bond 0.00307 (11829) covalent geometry : angle 0.63374 (15975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7477 (pm20) cc_final: 0.7218 (pm20) REVERT: A 33 ILE cc_start: 0.8528 (mm) cc_final: 0.8109 (tt) REVERT: A 47 LEU cc_start: 0.9015 (tp) cc_final: 0.8778 (tp) REVERT: A 52 ASP cc_start: 0.7557 (m-30) cc_final: 0.7345 (m-30) REVERT: A 64 LYS cc_start: 0.7897 (mmpt) cc_final: 0.7382 (mmtt) REVERT: A 75 LYS cc_start: 0.8574 (pptt) cc_final: 0.8322 (pttp) REVERT: B 97 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7685 (pp) REVERT: B 171 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8077 (pt) REVERT: B 237 TYR cc_start: 0.7530 (m-80) cc_final: 0.7255 (m-10) REVERT: C 197 ASP cc_start: 0.8345 (t70) cc_final: 0.8108 (t70) REVERT: C 287 ILE cc_start: 0.8924 (mt) cc_final: 0.8636 (mm) REVERT: C 377 MET cc_start: 0.7816 (mmm) cc_final: 0.7258 (mmm) REVERT: C 409 TYR cc_start: 0.6977 (m-80) cc_final: 0.6701 (m-80) REVERT: D 197 ASP cc_start: 0.7537 (p0) cc_final: 0.7140 (t0) REVERT: D 203 LYS cc_start: 0.8166 (pttm) cc_final: 0.7746 (ptpt) REVERT: D 225 GLN cc_start: 0.8084 (mp10) cc_final: 0.7641 (mp10) REVERT: D 429 MET cc_start: 0.7463 (mtt) cc_final: 0.6962 (mtt) REVERT: D 454 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7524 (tt) REVERT: E 201 LEU cc_start: 0.7619 (pt) cc_final: 0.7341 (pp) REVERT: E 221 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6965 (mp) REVERT: E 408 TRP cc_start: 0.8914 (m100) cc_final: 0.8282 (m-10) REVERT: E 453 GLN cc_start: 0.7714 (pp30) cc_final: 0.7458 (pp30) outliers start: 44 outliers final: 30 residues processed: 200 average time/residue: 0.3580 time to fit residues: 105.6667 Evaluate side-chains 196 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 0.0970 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.166809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129670 restraints weight = 19449.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.134061 restraints weight = 11590.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.136999 restraints weight = 8592.968| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 11866 Z= 0.300 Angle : 0.802 11.607 16053 Z= 0.409 Chirality : 0.050 0.235 1726 Planarity : 0.005 0.049 2046 Dihedral : 6.405 55.262 1700 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.05 % Allowed : 16.94 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.51 (0.21), residues: 592 loop : -1.71 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 177 HIS 0.006 0.002 HIS D 173 PHE 0.017 0.002 PHE B 130 TYR 0.019 0.002 TYR E 210 ARG 0.009 0.001 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 1.30013 ( 12) hydrogen bonds : bond 0.04891 ( 324) hydrogen bonds : angle 7.12525 ( 882) SS BOND : bond 0.00903 ( 33) SS BOND : angle 2.42593 ( 66) covalent geometry : bond 0.00695 (11829) covalent geometry : angle 0.78762 (15975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7543 (m-30) cc_final: 0.7250 (m-30) REVERT: A 75 LYS cc_start: 0.8621 (pptt) cc_final: 0.8372 (pttp) REVERT: B 171 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8201 (pt) REVERT: B 201 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6637 (tt) REVERT: B 227 SER cc_start: 0.8463 (t) cc_final: 0.8081 (m) REVERT: B 317 MET cc_start: 0.7825 (mtp) cc_final: 0.7617 (mtt) REVERT: C 163 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8964 (mttt) REVERT: C 201 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5824 (tt) REVERT: C 230 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7459 (m-40) REVERT: C 287 ILE cc_start: 0.9012 (mt) cc_final: 0.8719 (mm) REVERT: C 377 MET cc_start: 0.7892 (mmm) cc_final: 0.7525 (mmm) REVERT: D 429 MET cc_start: 0.7579 (mtt) cc_final: 0.7064 (mtt) REVERT: D 454 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7450 (tt) outliers start: 50 outliers final: 38 residues processed: 186 average time/residue: 0.2901 time to fit residues: 81.6375 Evaluate side-chains 185 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 210 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.170439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.134295 restraints weight = 18938.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.138920 restraints weight = 10967.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.141881 restraints weight = 7989.682| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 11866 Z= 0.151 Angle : 0.689 12.087 16053 Z= 0.348 Chirality : 0.047 0.220 1726 Planarity : 0.004 0.041 2046 Dihedral : 6.082 55.228 1700 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.48 % Allowed : 18.40 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.24 (0.22), residues: 559 loop : -1.60 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 36 HIS 0.005 0.001 HIS B 129 PHE 0.014 0.001 PHE B 130 TYR 0.019 0.002 TYR B 206 ARG 0.006 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 4) link_NAG-ASN : angle 1.13530 ( 12) hydrogen bonds : bond 0.03982 ( 324) hydrogen bonds : angle 6.73649 ( 882) SS BOND : bond 0.00751 ( 33) SS BOND : angle 1.76811 ( 66) covalent geometry : bond 0.00354 (11829) covalent geometry : angle 0.68054 (15975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8565 (pptt) cc_final: 0.8360 (pttp) REVERT: A 90 TYR cc_start: 0.6423 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: B 97 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7758 (pp) REVERT: B 171 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (pt) REVERT: B 201 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6667 (tt) REVERT: B 227 SER cc_start: 0.8534 (t) cc_final: 0.8045 (m) REVERT: C 163 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8950 (mttt) REVERT: C 287 ILE cc_start: 0.8946 (mt) cc_final: 0.8665 (mm) REVERT: C 409 TYR cc_start: 0.7004 (m-80) cc_final: 0.6779 (m-80) REVERT: D 203 LYS cc_start: 0.8216 (pttm) cc_final: 0.7937 (ptpt) REVERT: D 225 GLN cc_start: 0.8163 (mp10) cc_final: 0.7872 (mp10) REVERT: D 429 MET cc_start: 0.7482 (mtt) cc_final: 0.7035 (mtt) REVERT: E 201 LEU cc_start: 0.7637 (pt) cc_final: 0.7373 (pp) REVERT: E 408 TRP cc_start: 0.8913 (m-10) cc_final: 0.8297 (m-10) outliers start: 43 outliers final: 32 residues processed: 187 average time/residue: 0.2408 time to fit residues: 67.7494 Evaluate side-chains 194 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 210 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 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 = 0.4464 r_free = 0.4464 target = 0.168977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.132691 restraints weight = 19064.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.137251 restraints weight = 11164.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.140234 restraints weight = 8173.662| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11866 Z= 0.191 Angle : 0.720 11.574 16053 Z= 0.363 Chirality : 0.047 0.214 1726 Planarity : 0.004 0.042 2046 Dihedral : 6.127 54.861 1700 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.57 % Allowed : 18.80 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.31 (0.22), residues: 559 loop : -1.64 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 36 HIS 0.005 0.001 HIS B 129 PHE 0.015 0.001 PHE B 130 TYR 0.024 0.002 TYR B 206 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 4) link_NAG-ASN : angle 1.15378 ( 12) hydrogen bonds : bond 0.04149 ( 324) hydrogen bonds : angle 6.76310 ( 882) SS BOND : bond 0.00650 ( 33) SS BOND : angle 1.72009 ( 66) covalent geometry : bond 0.00449 (11829) covalent geometry : angle 0.71268 (15975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8589 (pptt) cc_final: 0.8368 (pttp) REVERT: A 90 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: B 97 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7811 (pp) REVERT: B 171 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8153 (pt) REVERT: B 201 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6532 (tt) REVERT: B 227 SER cc_start: 0.8499 (t) cc_final: 0.8121 (m) REVERT: C 163 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8973 (mttt) REVERT: C 201 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5816 (tt) REVERT: C 287 ILE cc_start: 0.8968 (mt) cc_final: 0.8678 (mm) REVERT: C 377 MET cc_start: 0.7835 (mmm) cc_final: 0.7451 (mmm) REVERT: D 203 LYS cc_start: 0.8250 (pttm) cc_final: 0.7922 (ptpt) REVERT: D 208 GLU cc_start: 0.7848 (tt0) cc_final: 0.7605 (tt0) REVERT: D 225 GLN cc_start: 0.8215 (mp10) cc_final: 0.7954 (mp10) REVERT: D 429 MET cc_start: 0.7521 (mtt) cc_final: 0.7090 (mtt) REVERT: E 201 LEU cc_start: 0.7566 (pt) cc_final: 0.7271 (pp) REVERT: E 408 TRP cc_start: 0.8951 (m-10) cc_final: 0.8329 (m-10) outliers start: 44 outliers final: 36 residues processed: 184 average time/residue: 0.3319 time to fit residues: 90.5977 Evaluate side-chains 196 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 210 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 0 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.166503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.129385 restraints weight = 19252.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.133654 restraints weight = 11606.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136511 restraints weight = 8693.449| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11866 Z= 0.285 Angle : 0.814 10.962 16053 Z= 0.415 Chirality : 0.051 0.220 1726 Planarity : 0.005 0.050 2046 Dihedral : 6.461 55.304 1700 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.57 % Allowed : 18.80 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.58 (0.21), residues: 586 loop : -1.78 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 36 HIS 0.006 0.001 HIS E 129 PHE 0.020 0.002 PHE B 130 TYR 0.021 0.002 TYR B 206 ARG 0.005 0.001 ARG B 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 1.32053 ( 12) hydrogen bonds : bond 0.04812 ( 324) hydrogen bonds : angle 7.07486 ( 882) SS BOND : bond 0.00751 ( 33) SS BOND : angle 1.96242 ( 66) covalent geometry : bond 0.00666 (11829) covalent geometry : angle 0.80519 (15975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8407 (mm) cc_final: 0.8148 (tp) REVERT: A 52 ASP cc_start: 0.8183 (m-30) cc_final: 0.7870 (m-30) REVERT: A 90 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.6276 (m-80) REVERT: B 171 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8182 (pt) REVERT: B 201 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6619 (tt) REVERT: B 227 SER cc_start: 0.8485 (t) cc_final: 0.8098 (m) REVERT: C 163 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8966 (mttt) REVERT: C 201 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5915 (tt) REVERT: C 287 ILE cc_start: 0.9005 (mt) cc_final: 0.8716 (mm) REVERT: C 377 MET cc_start: 0.7864 (mmm) cc_final: 0.7388 (mmm) REVERT: D 208 GLU cc_start: 0.7900 (tt0) cc_final: 0.7646 (tt0) REVERT: D 225 GLN cc_start: 0.8351 (mp10) cc_final: 0.8099 (mp10) REVERT: D 429 MET cc_start: 0.7561 (mtt) cc_final: 0.7101 (mtt) REVERT: D 454 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7533 (tt) REVERT: E 377 MET cc_start: 0.7967 (mmm) cc_final: 0.7073 (mmm) outliers start: 44 outliers final: 35 residues processed: 181 average time/residue: 0.2044 time to fit residues: 55.4192 Evaluate side-chains 188 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 210 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 47 optimal weight: 0.0570 chunk 70 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 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 = 0.4480 r_free = 0.4480 target = 0.171603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.134607 restraints weight = 18755.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.139314 restraints weight = 10972.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.142319 restraints weight = 8034.572| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11866 Z= 0.135 Angle : 0.691 11.647 16053 Z= 0.346 Chirality : 0.046 0.201 1726 Planarity : 0.004 0.042 2046 Dihedral : 6.047 55.059 1700 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.16 % Allowed : 19.69 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.32 (0.22), residues: 558 loop : -1.61 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 36 HIS 0.004 0.001 HIS B 129 PHE 0.010 0.001 PHE B 130 TYR 0.022 0.002 TYR B 206 ARG 0.003 0.000 ARG B 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 4) link_NAG-ASN : angle 1.17064 ( 12) hydrogen bonds : bond 0.03828 ( 324) hydrogen bonds : angle 6.62858 ( 882) SS BOND : bond 0.00552 ( 33) SS BOND : angle 1.48717 ( 66) covalent geometry : bond 0.00315 (11829) covalent geometry : angle 0.68499 (15975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4186.91 seconds wall clock time: 79 minutes 30.21 seconds (4770.21 seconds total)