Starting phenix.real_space_refine on Wed Jun 11 22:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zts_60471/06_2025/8zts_60471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zts_60471/06_2025/8zts_60471.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/8zts_60471/06_2025/8zts_60471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zts_60471/06_2025/8zts_60471.map" model { file = "/net/cci-nas-00/data/ceres_data/8zts_60471/06_2025/8zts_60471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zts_60471/06_2025/8zts_60471.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= 0.000 sd= 0.003 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 110 5.16 5 C 8765 2.51 5 N 2210 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "A" 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: "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: 8.22, per 1000 atoms: 0.61 Number of scatterers: 13515 At special positions: 0 Unit cell: (86.1, 83.64, 156.62, 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 110 16.00 O 2430 8.00 N 2210 7.00 C 8765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 161 " distance=2.03 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 A 501 " - " ASN A 132 " " NAG B 501 " - " ASN B 132 " " NAG C 501 " - " ASN C 132 " " NAG D 501 " - " ASN D 132 " " NAG E 501 " - " ASN E 132 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.7 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 25 sheets defined 43.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.952A pdb=" N GLU A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 217 through 238 removed outlier: 4.827A pdb=" N LEU A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 279 through 308 Processing helix chain 'A' and resid 351 through 405 removed outlier: 3.609A pdb=" N VAL A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.861A pdb=" N GLU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 224 through 238 removed outlier: 3.598A pdb=" N THR B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 248 through 269 removed outlier: 3.812A pdb=" N GLN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 308 removed outlier: 4.519A pdb=" N ILE B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 405 removed outlier: 3.534A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.919A pdb=" N GLU C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.588A pdb=" N THR C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 248 through 268 Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 351 through 405 removed outlier: 3.626A pdb=" N VAL C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.931A pdb=" N GLU D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 87 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 238 removed outlier: 3.518A pdb=" N THR D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.525A pdb=" N LEU D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 308 Processing helix chain 'D' and resid 351 through 405 removed outlier: 3.624A pdb=" N VAL D 356 " --> pdb=" O MET D 352 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.947A pdb=" N GLU E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 217 through 224 Processing helix chain 'E' and resid 224 through 238 removed outlier: 3.604A pdb=" N THR E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 248 through 268 Processing helix chain 'E' and resid 278 through 308 removed outlier: 4.470A pdb=" N ILE E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 303 " --> pdb=" O MET E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 406 removed outlier: 3.547A pdb=" N VAL E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.225A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 144 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER A 117 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.225A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 70 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 64 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 164 removed outlier: 6.827A pdb=" N PHE A 208 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 199 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 210 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 197 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 212 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 194 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 187 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 8.206A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 144 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER B 117 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 101 removed outlier: 8.206A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 70 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL B 64 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 72 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 164 removed outlier: 6.978A pdb=" N PHE B 208 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU B 199 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 210 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 197 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 212 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 101 removed outlier: 8.173A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU C 144 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER C 117 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 101 removed outlier: 8.173A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG C 70 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 64 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C 72 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AB6, first strand: chain 'C' and resid 158 through 164 removed outlier: 6.934A pdb=" N PHE C 208 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU C 199 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA C 210 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C 197 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 212 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 194 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 187 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 101 removed outlier: 8.082A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 144 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER D 117 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 97 through 101 removed outlier: 8.082A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG D 70 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 64 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN D 72 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 164 removed outlier: 6.952A pdb=" N PHE D 208 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 199 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA D 210 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 197 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY D 212 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.208A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 144 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER E 117 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.208A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG E 70 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL E 64 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN E 72 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 164 removed outlier: 6.939A pdb=" N PHE E 208 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU E 199 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA E 210 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 197 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY E 212 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR E 194 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY E 187 " --> pdb=" O THR E 194 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2412 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: 4.15 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4278 1.34 - 1.46: 2959 1.46 - 1.58: 6378 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 13790 Sorted by residual: bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 ... (remaining 13785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18565 2.19 - 4.39: 187 4.39 - 6.58: 30 6.58 - 8.78: 7 8.78 - 10.97: 1 Bond angle restraints: 18790 Sorted by residual: angle pdb=" CB MET A 39 " pdb=" CG MET A 39 " pdb=" SD MET A 39 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET D 39 " pdb=" CG MET D 39 " pdb=" SD MET D 39 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" C ASN C 153 " pdb=" N TYR C 154 " pdb=" CA TYR C 154 " ideal model delta sigma weight residual 120.69 112.57 8.12 2.95e+00 1.15e-01 7.58e+00 angle pdb=" C ASN B 153 " pdb=" N TYR B 154 " pdb=" CA TYR B 154 " ideal model delta sigma weight residual 120.69 112.79 7.90 2.95e+00 1.15e-01 7.18e+00 angle pdb=" CB MET C 39 " pdb=" CG MET C 39 " pdb=" SD MET C 39 " ideal model delta sigma weight residual 112.70 120.67 -7.97 3.00e+00 1.11e-01 7.05e+00 ... (remaining 18785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7152 17.65 - 35.30: 911 35.30 - 52.95: 220 52.95 - 70.60: 34 70.60 - 88.25: 23 Dihedral angle restraints: 8340 sinusoidal: 3235 harmonic: 5105 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 161 " pdb=" CB CYS B 161 " ideal model delta sinusoidal sigma weight residual 93.00 161.78 -68.78 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 161 " pdb=" CB CYS A 161 " ideal model delta sinusoidal sigma weight residual 93.00 160.70 -67.70 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 161 " pdb=" CB CYS D 161 " ideal model delta sinusoidal sigma weight residual 93.00 159.69 -66.69 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1581 0.037 - 0.073: 503 0.073 - 0.110: 161 0.110 - 0.147: 41 0.147 - 0.183: 4 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CB THR C 358 " pdb=" CA THR C 358 " pdb=" OG1 THR C 358 " pdb=" CG2 THR C 358 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CG LEU B 391 " pdb=" CB LEU B 391 " pdb=" CD1 LEU B 391 " pdb=" CD2 LEU B 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CG LEU C 391 " pdb=" CB LEU C 391 " pdb=" CD1 LEU C 391 " pdb=" CD2 LEU C 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2287 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 109 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C VAL E 109 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL E 109 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU E 110 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 125 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C ASN C 125 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN C 125 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP C 126 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 237 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL E 237 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL E 237 " -0.009 2.00e-02 2.50e+03 pdb=" N SER E 238 " -0.008 2.00e-02 2.50e+03 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1981 2.76 - 3.29: 12645 3.29 - 3.83: 22761 3.83 - 4.36: 24732 4.36 - 4.90: 44571 Nonbonded interactions: 106690 Sorted by model distance: nonbonded pdb=" O ASN E 125 " pdb=" ND2 ASN E 125 " model vdw 2.225 3.120 nonbonded pdb=" O ASN C 125 " pdb=" ND2 ASN C 125 " model vdw 2.226 3.120 nonbonded pdb=" O THR A 25 " pdb=" OH TYR A 95 " model vdw 2.274 3.040 nonbonded pdb=" O THR D 25 " pdb=" OH TYR D 95 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP B 83 " pdb=" NH1 ARG C 28 " model vdw 2.287 3.120 ... (remaining 106685 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.830 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.660 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.003 0.027 13805 Z= 0.144 Angle : 0.609 10.971 18825 Z= 0.311 Chirality : 0.042 0.183 2290 Planarity : 0.004 0.037 2345 Dihedral : 16.786 88.254 4990 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.61 % Allowed : 24.73 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.19 (0.21), residues: 1720 helix: 2.69 (0.19), residues: 695 sheet: 0.06 (0.25), residues: 465 loop : -1.01 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 81 HIS 0.004 0.001 HIS D 122 PHE 0.021 0.001 PHE E 387 TYR 0.006 0.001 TYR C 217 ARG 0.008 0.001 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 5) link_NAG-ASN : angle 0.77080 ( 15) hydrogen bonds : bond 0.10947 ( 777) hydrogen bonds : angle 5.19891 ( 2412) SS BOND : bond 0.00174 ( 10) SS BOND : angle 0.51073 ( 20) covalent geometry : bond 0.00297 (13790) covalent geometry : angle 0.60884 (18790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 282 time to evaluate : 1.444 Fit side-chains REVERT: E 223 THR cc_start: 0.7487 (t) cc_final: 0.7281 (m) outliers start: 9 outliers final: 4 residues processed: 287 average time/residue: 0.2564 time to fit residues: 106.3035 Evaluate side-chains 266 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 235 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN C 125 ASN D 193 GLN D 216 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.097742 restraints weight = 19354.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.100771 restraints weight = 10360.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102761 restraints weight = 6746.839| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13805 Z= 0.169 Angle : 0.594 7.407 18825 Z= 0.298 Chirality : 0.043 0.194 2290 Planarity : 0.004 0.030 2345 Dihedral : 4.438 37.398 1958 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.92 % Allowed : 22.97 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1720 helix: 2.78 (0.19), residues: 685 sheet: -0.03 (0.25), residues: 480 loop : -1.07 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 81 HIS 0.003 0.001 HIS D 122 PHE 0.022 0.002 PHE E 359 TYR 0.010 0.001 TYR E 130 ARG 0.004 0.001 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 5) link_NAG-ASN : angle 1.46443 ( 15) hydrogen bonds : bond 0.05364 ( 777) hydrogen bonds : angle 4.45922 ( 2412) SS BOND : bond 0.00301 ( 10) SS BOND : angle 0.68360 ( 20) covalent geometry : bond 0.00386 (13790) covalent geometry : angle 0.59224 (18790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 1.580 Fit side-chains REVERT: A 386 LEU cc_start: 0.7681 (mm) cc_final: 0.7474 (mp) REVERT: A 391 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 181 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: C 166 GLU cc_start: 0.7168 (tp30) cc_final: 0.6887 (tt0) REVERT: C 295 MET cc_start: 0.8194 (ttp) cc_final: 0.7842 (ttp) REVERT: C 374 HIS cc_start: 0.7660 (m170) cc_final: 0.7435 (m170) REVERT: D 399 MET cc_start: 0.8131 (tpp) cc_final: 0.7722 (tpt) REVERT: E 166 GLU cc_start: 0.7026 (tp30) cc_final: 0.6715 (tt0) REVERT: E 181 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: E 374 HIS cc_start: 0.7652 (m170) cc_final: 0.7404 (m170) REVERT: E 400 LEU cc_start: 0.7798 (tt) cc_final: 0.7594 (tt) outliers start: 58 outliers final: 37 residues processed: 301 average time/residue: 0.2536 time to fit residues: 111.2083 Evaluate side-chains 295 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 110 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.097642 restraints weight = 19499.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100722 restraints weight = 10415.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.102758 restraints weight = 6764.394| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13805 Z= 0.134 Angle : 0.537 6.714 18825 Z= 0.273 Chirality : 0.041 0.160 2290 Planarity : 0.003 0.031 2345 Dihedral : 4.148 35.371 1953 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.59 % Allowed : 23.31 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1720 helix: 2.89 (0.19), residues: 685 sheet: -0.13 (0.25), residues: 480 loop : -1.13 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.002 0.001 HIS B 122 PHE 0.024 0.001 PHE D 387 TYR 0.008 0.001 TYR E 217 ARG 0.005 0.000 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 1.16148 ( 15) hydrogen bonds : bond 0.04974 ( 777) hydrogen bonds : angle 4.27597 ( 2412) SS BOND : bond 0.00242 ( 10) SS BOND : angle 0.56883 ( 20) covalent geometry : bond 0.00298 (13790) covalent geometry : angle 0.53624 (18790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 1.621 Fit side-chains REVERT: A 386 LEU cc_start: 0.7632 (mm) cc_final: 0.7420 (mp) REVERT: A 391 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7605 (mp) REVERT: B 125 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7749 (t0) REVERT: B 270 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7487 (mp) REVERT: C 166 GLU cc_start: 0.7132 (tp30) cc_final: 0.6859 (tt0) REVERT: C 295 MET cc_start: 0.8141 (ttp) cc_final: 0.7825 (ttp) REVERT: C 374 HIS cc_start: 0.7679 (m170) cc_final: 0.7446 (m170) REVERT: D 262 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7612 (t80) REVERT: D 310 LEU cc_start: 0.7434 (mp) cc_final: 0.6624 (pp) REVERT: D 399 MET cc_start: 0.8136 (tpp) cc_final: 0.7705 (tpt) REVERT: E 39 MET cc_start: 0.7898 (mmp) cc_final: 0.7437 (mmm) REVERT: E 166 GLU cc_start: 0.7138 (tp30) cc_final: 0.6877 (tt0) REVERT: E 181 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: E 230 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7815 (mm) REVERT: E 374 HIS cc_start: 0.7683 (m170) cc_final: 0.7446 (m170) outliers start: 68 outliers final: 42 residues processed: 313 average time/residue: 0.2510 time to fit residues: 114.9448 Evaluate side-chains 306 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 7.9990 chunk 138 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN C 137 HIS ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.089848 restraints weight = 20188.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092902 restraints weight = 10545.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094893 restraints weight = 6739.628| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13805 Z= 0.138 Angle : 0.543 7.687 18825 Z= 0.274 Chirality : 0.041 0.163 2290 Planarity : 0.003 0.034 2345 Dihedral : 4.133 35.675 1953 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.74 % Allowed : 23.18 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.11 (0.21), residues: 1720 helix: 2.87 (0.19), residues: 685 sheet: -0.20 (0.25), residues: 480 loop : -1.16 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.002 0.001 HIS E 122 PHE 0.014 0.001 PHE B 359 TYR 0.016 0.001 TYR D 59 ARG 0.005 0.000 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 5) link_NAG-ASN : angle 1.25904 ( 15) hydrogen bonds : bond 0.04970 ( 777) hydrogen bonds : angle 4.21976 ( 2412) SS BOND : bond 0.00253 ( 10) SS BOND : angle 0.56083 ( 20) covalent geometry : bond 0.00308 (13790) covalent geometry : angle 0.54181 (18790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 271 time to evaluate : 1.549 Fit side-chains REVERT: A 386 LEU cc_start: 0.7558 (mm) cc_final: 0.7333 (mp) REVERT: A 391 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7503 (mp) REVERT: B 125 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7779 (t0) REVERT: B 181 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: B 270 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7475 (mp) REVERT: C 125 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7738 (t0) REVERT: C 166 GLU cc_start: 0.7191 (tp30) cc_final: 0.6822 (tt0) REVERT: C 295 MET cc_start: 0.8144 (ttp) cc_final: 0.7756 (ttp) REVERT: C 374 HIS cc_start: 0.7723 (m170) cc_final: 0.7508 (m170) REVERT: D 233 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8060 (tt) REVERT: D 262 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7601 (t80) REVERT: D 310 LEU cc_start: 0.7572 (mp) cc_final: 0.6655 (pp) REVERT: D 399 MET cc_start: 0.8114 (tpp) cc_final: 0.7688 (tpt) REVERT: E 166 GLU cc_start: 0.7153 (tp30) cc_final: 0.6868 (tt0) REVERT: E 181 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: E 230 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7798 (mm) REVERT: E 262 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7596 (t80) REVERT: E 368 ASN cc_start: 0.6094 (OUTLIER) cc_final: 0.5857 (t0) REVERT: E 374 HIS cc_start: 0.7663 (m170) cc_final: 0.7412 (m170) outliers start: 85 outliers final: 57 residues processed: 330 average time/residue: 0.2330 time to fit residues: 113.9639 Evaluate side-chains 325 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 193 GLN E 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090682 restraints weight = 20175.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.093821 restraints weight = 10275.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095918 restraints weight = 6491.865| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13805 Z= 0.225 Angle : 0.662 8.215 18825 Z= 0.333 Chirality : 0.045 0.198 2290 Planarity : 0.004 0.039 2345 Dihedral : 4.704 50.341 1953 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 7.03 % Allowed : 24.19 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1720 helix: 2.49 (0.19), residues: 660 sheet: -0.48 (0.24), residues: 480 loop : -1.34 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 81 HIS 0.004 0.001 HIS D 122 PHE 0.020 0.002 PHE E 236 TYR 0.016 0.002 TYR D 59 ARG 0.009 0.001 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 5) link_NAG-ASN : angle 2.05591 ( 15) hydrogen bonds : bond 0.05956 ( 777) hydrogen bonds : angle 4.56499 ( 2412) SS BOND : bond 0.00404 ( 10) SS BOND : angle 0.80263 ( 20) covalent geometry : bond 0.00526 (13790) covalent geometry : angle 0.65912 (18790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 254 time to evaluate : 1.452 Fit side-chains REVERT: A 364 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6498 (m-30) REVERT: A 386 LEU cc_start: 0.7520 (mm) cc_final: 0.7260 (mp) REVERT: A 391 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7489 (mp) REVERT: B 181 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6865 (tt0) REVERT: B 270 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7710 (mp) REVERT: C 125 ASN cc_start: 0.7984 (t160) cc_final: 0.7736 (t0) REVERT: C 166 GLU cc_start: 0.7262 (tp30) cc_final: 0.6887 (tt0) REVERT: C 230 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7873 (mm) REVERT: C 262 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7791 (t80) REVERT: C 310 LEU cc_start: 0.7668 (mt) cc_final: 0.7366 (mt) REVERT: C 374 HIS cc_start: 0.7726 (m170) cc_final: 0.7521 (m170) REVERT: D 262 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7594 (t80) REVERT: D 310 LEU cc_start: 0.7621 (mp) cc_final: 0.7026 (pp) REVERT: D 371 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6077 (mp0) REVERT: D 374 HIS cc_start: 0.7773 (m170) cc_final: 0.7437 (m170) REVERT: D 399 MET cc_start: 0.8059 (tpp) cc_final: 0.7697 (tpt) REVERT: E 166 GLU cc_start: 0.7250 (tp30) cc_final: 0.6756 (tt0) REVERT: E 181 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: E 230 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7746 (mm) REVERT: E 262 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7613 (t80) REVERT: E 371 GLU cc_start: 0.6714 (tm-30) cc_final: 0.5962 (mp0) REVERT: E 374 HIS cc_start: 0.7579 (m170) cc_final: 0.7304 (m170) outliers start: 104 outliers final: 77 residues processed: 333 average time/residue: 0.2487 time to fit residues: 124.2332 Evaluate side-chains 341 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 254 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092465 restraints weight = 20030.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095655 restraints weight = 10355.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097778 restraints weight = 6573.106| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13805 Z= 0.175 Angle : 0.597 10.205 18825 Z= 0.303 Chirality : 0.043 0.172 2290 Planarity : 0.004 0.032 2345 Dihedral : 4.524 48.693 1953 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 7.36 % Allowed : 24.66 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1720 helix: 2.44 (0.19), residues: 685 sheet: -0.53 (0.24), residues: 480 loop : -1.32 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 81 HIS 0.003 0.001 HIS D 122 PHE 0.018 0.002 PHE E 236 TYR 0.013 0.001 TYR D 59 ARG 0.006 0.001 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 5) link_NAG-ASN : angle 1.66093 ( 15) hydrogen bonds : bond 0.05513 ( 777) hydrogen bonds : angle 4.42766 ( 2412) SS BOND : bond 0.00311 ( 10) SS BOND : angle 0.85040 ( 20) covalent geometry : bond 0.00401 (13790) covalent geometry : angle 0.59521 (18790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 255 time to evaluate : 1.728 Fit side-chains REVERT: A 386 LEU cc_start: 0.7504 (mm) cc_final: 0.7251 (mp) REVERT: A 391 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7446 (mp) REVERT: B 181 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: B 224 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7382 (mp) REVERT: B 270 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7591 (mp) REVERT: C 125 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7606 (t0) REVERT: C 166 GLU cc_start: 0.7197 (tp30) cc_final: 0.6812 (tt0) REVERT: C 262 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7724 (t80) REVERT: C 310 LEU cc_start: 0.7678 (mt) cc_final: 0.7379 (mt) REVERT: D 233 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7972 (tt) REVERT: D 262 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7545 (t80) REVERT: D 310 LEU cc_start: 0.7674 (mp) cc_final: 0.7348 (mt) REVERT: D 371 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6025 (mp0) REVERT: D 374 HIS cc_start: 0.7777 (m170) cc_final: 0.7473 (m170) REVERT: D 399 MET cc_start: 0.8075 (tpp) cc_final: 0.7655 (tpt) REVERT: E 166 GLU cc_start: 0.7249 (tp30) cc_final: 0.6733 (tt0) REVERT: E 230 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7786 (mm) REVERT: E 262 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7575 (t80) REVERT: E 368 ASN cc_start: 0.7072 (t0) cc_final: 0.6852 (t0) REVERT: E 371 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6057 (mp0) REVERT: E 374 HIS cc_start: 0.7647 (m170) cc_final: 0.7411 (m170) outliers start: 109 outliers final: 82 residues processed: 337 average time/residue: 0.2182 time to fit residues: 111.8461 Evaluate side-chains 346 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 254 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.089305 restraints weight = 20488.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.092568 restraints weight = 10174.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094698 restraints weight = 6325.188| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13805 Z= 0.143 Angle : 0.559 11.265 18825 Z= 0.283 Chirality : 0.042 0.158 2290 Planarity : 0.003 0.030 2345 Dihedral : 4.316 45.065 1953 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 7.23 % Allowed : 25.68 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1720 helix: 2.74 (0.19), residues: 680 sheet: -0.47 (0.25), residues: 480 loop : -1.32 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.003 0.001 HIS D 122 PHE 0.014 0.001 PHE E 236 TYR 0.013 0.001 TYR D 59 ARG 0.006 0.000 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 5) link_NAG-ASN : angle 1.39129 ( 15) hydrogen bonds : bond 0.05143 ( 777) hydrogen bonds : angle 4.30096 ( 2412) SS BOND : bond 0.00256 ( 10) SS BOND : angle 0.84421 ( 20) covalent geometry : bond 0.00322 (13790) covalent geometry : angle 0.55722 (18790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 261 time to evaluate : 1.695 Fit side-chains REVERT: A 386 LEU cc_start: 0.7472 (mm) cc_final: 0.7216 (mp) REVERT: A 391 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7421 (mp) REVERT: B 181 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: B 224 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7375 (mp) REVERT: B 270 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7513 (mp) REVERT: B 363 LEU cc_start: 0.6348 (mt) cc_final: 0.5854 (tp) REVERT: C 125 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7601 (t0) REVERT: C 166 GLU cc_start: 0.7204 (tp30) cc_final: 0.6820 (tt0) REVERT: C 262 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7653 (t80) REVERT: C 310 LEU cc_start: 0.7718 (mt) cc_final: 0.7416 (mt) REVERT: C 353 LEU cc_start: 0.6547 (tp) cc_final: 0.6178 (mp) REVERT: C 380 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7721 (mp) REVERT: D 233 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7975 (tt) REVERT: D 371 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6098 (mp0) REVERT: D 374 HIS cc_start: 0.7741 (m170) cc_final: 0.7453 (m170) REVERT: D 399 MET cc_start: 0.8127 (tpp) cc_final: 0.7640 (tpt) REVERT: E 111 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: E 166 GLU cc_start: 0.7241 (tp30) cc_final: 0.6730 (tt0) REVERT: E 170 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7673 (p) REVERT: E 230 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7808 (mm) REVERT: E 262 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7564 (t80) REVERT: E 310 LEU cc_start: 0.7601 (mt) cc_final: 0.6631 (pp) REVERT: E 371 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6149 (mp0) REVERT: E 374 HIS cc_start: 0.7660 (m170) cc_final: 0.7404 (m170) REVERT: E 387 PHE cc_start: 0.7882 (t80) cc_final: 0.7488 (t80) outliers start: 107 outliers final: 83 residues processed: 339 average time/residue: 0.2700 time to fit residues: 139.5594 Evaluate side-chains 354 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 259 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092472 restraints weight = 20166.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.095795 restraints weight = 10103.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.098007 restraints weight = 6273.777| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13805 Z= 0.134 Angle : 0.556 12.139 18825 Z= 0.280 Chirality : 0.041 0.172 2290 Planarity : 0.003 0.033 2345 Dihedral : 4.193 41.469 1953 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.82 % Allowed : 26.15 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1720 helix: 2.78 (0.19), residues: 685 sheet: -0.40 (0.25), residues: 480 loop : -1.26 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.003 0.001 HIS D 122 PHE 0.015 0.001 PHE B 359 TYR 0.013 0.001 TYR D 59 ARG 0.008 0.000 ARG B 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00004 ( 5) link_NAG-ASN : angle 1.27579 ( 15) hydrogen bonds : bond 0.05000 ( 777) hydrogen bonds : angle 4.23666 ( 2412) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.02725 ( 20) covalent geometry : bond 0.00301 (13790) covalent geometry : angle 0.55452 (18790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 265 time to evaluate : 2.309 Fit side-chains REVERT: A 386 LEU cc_start: 0.7563 (mm) cc_final: 0.7325 (mp) REVERT: A 391 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7412 (mp) REVERT: B 27 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7214 (ttp-170) REVERT: B 181 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: B 224 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7313 (mp) REVERT: B 270 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7466 (mp) REVERT: B 362 ARG cc_start: 0.5637 (mtp-110) cc_final: 0.5296 (ttp80) REVERT: C 125 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7719 (t0) REVERT: C 166 GLU cc_start: 0.7204 (tp30) cc_final: 0.6827 (tt0) REVERT: C 236 PHE cc_start: 0.7530 (m-10) cc_final: 0.7327 (m-10) REVERT: C 262 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7681 (t80) REVERT: C 310 LEU cc_start: 0.7719 (mt) cc_final: 0.7425 (mt) REVERT: C 353 LEU cc_start: 0.6533 (tp) cc_final: 0.6197 (mp) REVERT: C 380 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7723 (mp) REVERT: D 233 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8020 (tt) REVERT: D 374 HIS cc_start: 0.7752 (m170) cc_final: 0.7469 (m170) REVERT: D 399 MET cc_start: 0.8150 (tpp) cc_final: 0.7603 (tpt) REVERT: E 111 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7133 (pt0) REVERT: E 166 GLU cc_start: 0.7242 (tp30) cc_final: 0.6754 (tt0) REVERT: E 170 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7679 (p) REVERT: E 230 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7810 (mm) REVERT: E 262 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7616 (t80) REVERT: E 310 LEU cc_start: 0.7585 (mt) cc_final: 0.6458 (pp) REVERT: E 374 HIS cc_start: 0.7657 (m170) cc_final: 0.7423 (m170) outliers start: 101 outliers final: 83 residues processed: 337 average time/residue: 0.3448 time to fit residues: 180.4413 Evaluate side-chains 353 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 258 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095420 restraints weight = 19844.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098474 restraints weight = 10453.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100504 restraints weight = 6748.785| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13805 Z= 0.117 Angle : 0.540 12.687 18825 Z= 0.269 Chirality : 0.041 0.167 2290 Planarity : 0.003 0.036 2345 Dihedral : 4.018 35.970 1953 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.81 % Allowed : 27.09 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1720 helix: 2.91 (0.19), residues: 690 sheet: -0.21 (0.26), residues: 435 loop : -1.47 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.002 0.001 HIS D 122 PHE 0.018 0.001 PHE B 359 TYR 0.013 0.001 TYR D 59 ARG 0.008 0.000 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 5) link_NAG-ASN : angle 1.11808 ( 15) hydrogen bonds : bond 0.04706 ( 777) hydrogen bonds : angle 4.13626 ( 2412) SS BOND : bond 0.00244 ( 10) SS BOND : angle 0.87317 ( 20) covalent geometry : bond 0.00258 (13790) covalent geometry : angle 0.53851 (18790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 268 time to evaluate : 3.045 Fit side-chains REVERT: A 386 LEU cc_start: 0.7489 (mm) cc_final: 0.7247 (mp) REVERT: A 391 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7373 (mp) REVERT: B 181 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: B 224 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7252 (mp) REVERT: B 270 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 362 ARG cc_start: 0.5559 (mtp-110) cc_final: 0.5186 (ttp80) REVERT: B 363 LEU cc_start: 0.6330 (mt) cc_final: 0.5871 (tp) REVERT: C 125 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7714 (t0) REVERT: C 166 GLU cc_start: 0.7190 (tp30) cc_final: 0.6836 (tt0) REVERT: C 310 LEU cc_start: 0.7724 (mt) cc_final: 0.7470 (mt) REVERT: D 233 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7957 (tt) REVERT: D 371 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6092 (mp0) REVERT: D 399 MET cc_start: 0.8181 (tpp) cc_final: 0.7611 (tpt) REVERT: E 166 GLU cc_start: 0.7243 (tp30) cc_final: 0.6751 (tt0) REVERT: E 170 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7742 (p) REVERT: E 230 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7771 (mm) REVERT: E 262 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7535 (t80) REVERT: E 310 LEU cc_start: 0.7518 (mt) cc_final: 0.7256 (mp) REVERT: E 362 ARG cc_start: 0.5617 (mtp-110) cc_final: 0.4561 (mtt90) REVERT: E 371 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6054 (mp0) REVERT: E 374 HIS cc_start: 0.7607 (m170) cc_final: 0.7370 (m170) outliers start: 86 outliers final: 66 residues processed: 326 average time/residue: 0.3337 time to fit residues: 166.4272 Evaluate side-chains 337 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 262 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 137 HIS ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 125 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 267 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.090330 restraints weight = 20350.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.093374 restraints weight = 10631.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095359 restraints weight = 6800.794| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13805 Z= 0.128 Angle : 0.558 13.520 18825 Z= 0.278 Chirality : 0.041 0.168 2290 Planarity : 0.003 0.034 2345 Dihedral : 3.992 36.131 1951 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.95 % Allowed : 27.16 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1720 helix: 2.88 (0.19), residues: 690 sheet: -0.19 (0.26), residues: 435 loop : -1.44 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.003 0.001 HIS D 122 PHE 0.020 0.001 PHE B 359 TYR 0.021 0.001 TYR D 59 ARG 0.007 0.000 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 5) link_NAG-ASN : angle 1.19557 ( 15) hydrogen bonds : bond 0.04800 ( 777) hydrogen bonds : angle 4.15396 ( 2412) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.82857 ( 20) covalent geometry : bond 0.00284 (13790) covalent geometry : angle 0.55660 (18790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 267 time to evaluate : 1.877 Fit side-chains REVERT: A 386 LEU cc_start: 0.7564 (mm) cc_final: 0.7332 (mp) REVERT: A 391 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7429 (mp) REVERT: B 181 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: B 224 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 270 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7425 (mp) REVERT: B 362 ARG cc_start: 0.5536 (mtp-110) cc_final: 0.5158 (ttp80) REVERT: B 363 LEU cc_start: 0.6381 (mt) cc_final: 0.5913 (tp) REVERT: C 34 LEU cc_start: 0.8880 (mp) cc_final: 0.8633 (mp) REVERT: C 125 ASN cc_start: 0.7931 (t0) cc_final: 0.7672 (t0) REVERT: C 166 GLU cc_start: 0.7168 (tp30) cc_final: 0.6861 (tt0) REVERT: C 310 LEU cc_start: 0.7725 (mt) cc_final: 0.7487 (mt) REVERT: C 380 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7761 (mp) REVERT: D 99 MET cc_start: 0.6756 (ttm) cc_final: 0.6386 (ttp) REVERT: D 233 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8101 (tt) REVERT: D 399 MET cc_start: 0.8178 (tpp) cc_final: 0.7574 (tpt) REVERT: E 166 GLU cc_start: 0.7252 (tp30) cc_final: 0.6819 (tt0) REVERT: E 170 SER cc_start: 0.8146 (OUTLIER) cc_final: 0.7769 (p) REVERT: E 230 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7846 (mm) REVERT: E 262 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7580 (t80) REVERT: E 310 LEU cc_start: 0.7558 (mt) cc_final: 0.7274 (mt) REVERT: E 362 ARG cc_start: 0.5691 (mtp-110) cc_final: 0.5099 (ptm-80) REVERT: E 371 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6065 (mp0) REVERT: E 374 HIS cc_start: 0.7644 (m170) cc_final: 0.7409 (m170) outliers start: 88 outliers final: 72 residues processed: 331 average time/residue: 0.2575 time to fit residues: 128.4368 Evaluate side-chains 344 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 103 optimal weight: 0.0270 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.090419 restraints weight = 20370.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.093661 restraints weight = 10091.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.095848 restraints weight = 6275.633| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13805 Z= 0.137 Angle : 0.568 13.127 18825 Z= 0.283 Chirality : 0.042 0.174 2290 Planarity : 0.003 0.033 2345 Dihedral : 4.065 38.960 1951 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.08 % Allowed : 27.03 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1720 helix: 2.79 (0.19), residues: 690 sheet: -0.21 (0.26), residues: 435 loop : -1.45 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.003 0.001 HIS D 122 PHE 0.021 0.001 PHE B 359 TYR 0.020 0.001 TYR D 59 ARG 0.007 0.000 ARG E 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00004 ( 5) link_NAG-ASN : angle 1.27748 ( 15) hydrogen bonds : bond 0.04918 ( 777) hydrogen bonds : angle 4.19706 ( 2412) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.83349 ( 20) covalent geometry : bond 0.00308 (13790) covalent geometry : angle 0.56686 (18790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.10 seconds wall clock time: 85 minutes 53.88 seconds (5153.88 seconds total)