Starting phenix.real_space_refine on Thu Sep 18 02:20:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zts_60471/09_2025/8zts_60471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zts_60471/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zts_60471/09_2025/8zts_60471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zts_60471/09_2025/8zts_60471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zts_60471/09_2025/8zts_60471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zts_60471/09_2025/8zts_60471.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: 3.59, per 1000 atoms: 0.27 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: 1.08 Conformation dependent library (CDL) restraints added in 664.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.43 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: 2.35 Time building geometry restraints manager: 1.47 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: 0.01 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: 1.130 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- 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 : 7.40 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG E 362 TYR 0.006 0.001 TYR C 217 PHE 0.021 0.001 PHE E 387 TRP 0.011 0.002 TRP D 81 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00297 (13790) covalent geometry : angle 0.60884 (18790) SS BOND : bond 0.00174 ( 10) SS BOND : angle 0.51073 ( 20) hydrogen bonds : bond 0.10947 ( 777) hydrogen bonds : angle 5.19891 ( 2412) link_NAG-ASN : bond 0.00111 ( 5) link_NAG-ASN : angle 0.77080 ( 15) *********************** 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 : 0.540 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: 0.1227 time to fit residues: 50.8199 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 : 0.508 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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** C 125 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.098621 restraints weight = 19404.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101679 restraints weight = 10315.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103700 restraints weight = 6690.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105071 restraints weight = 4971.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105846 restraints weight = 4055.563| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13805 Z= 0.110 Angle : 0.509 6.550 18825 Z= 0.258 Chirality : 0.040 0.153 2290 Planarity : 0.003 0.030 2345 Dihedral : 4.067 29.916 1958 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.77 % Allowed : 23.11 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1720 helix: 3.07 (0.19), residues: 695 sheet: 0.21 (0.26), residues: 480 loop : -0.86 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 362 TYR 0.006 0.001 TYR D 217 PHE 0.024 0.001 PHE E 359 TRP 0.010 0.001 TRP E 81 HIS 0.002 0.000 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00232 (13790) covalent geometry : angle 0.50877 (18790) SS BOND : bond 0.00178 ( 10) SS BOND : angle 0.45829 ( 20) hydrogen bonds : bond 0.04585 ( 777) hydrogen bonds : angle 4.23158 ( 2412) link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 1.02017 ( 15) *********************** 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 330 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 0.348 Fit side-chains REVERT: A 236 PHE cc_start: 0.7387 (m-10) cc_final: 0.7177 (m-80) REVERT: A 391 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7576 (mp) REVERT: B 243 LEU cc_start: 0.8147 (mp) cc_final: 0.7938 (mt) REVERT: B 362 ARG cc_start: 0.6353 (ttm-80) cc_final: 0.5554 (ttp80) REVERT: C 166 GLU cc_start: 0.7219 (tp30) cc_final: 0.6898 (tt0) REVERT: C 295 MET cc_start: 0.8157 (ttp) cc_final: 0.7748 (ttp) REVERT: D 387 PHE cc_start: 0.7613 (t80) cc_final: 0.7382 (t80) REVERT: E 39 MET cc_start: 0.7728 (mmp) cc_final: 0.7413 (mmm) REVERT: E 166 GLU cc_start: 0.6985 (tp30) cc_final: 0.6730 (tt0) REVERT: E 181 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: E 374 HIS cc_start: 0.7613 (m170) cc_final: 0.7399 (m170) outliers start: 41 outliers final: 27 residues processed: 315 average time/residue: 0.1069 time to fit residues: 49.6058 Evaluate side-chains 297 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR 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 235 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 400 LEU 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 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 159 ASP 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 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 132 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 A 137 HIS C 137 HIS D 193 GLN D 216 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 193 GLN E 216 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095556 restraints weight = 19591.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.098713 restraints weight = 10217.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100790 restraints weight = 6539.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102172 restraints weight = 4834.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102971 restraints weight = 3919.590| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13805 Z= 0.221 Angle : 0.662 8.395 18825 Z= 0.333 Chirality : 0.045 0.212 2290 Planarity : 0.004 0.030 2345 Dihedral : 4.509 29.403 1952 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.95 % Allowed : 22.70 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1720 helix: 2.49 (0.18), residues: 680 sheet: -0.25 (0.25), residues: 480 loop : -1.23 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 354 TYR 0.014 0.002 TYR D 59 PHE 0.015 0.002 PHE B 251 TRP 0.012 0.002 TRP E 106 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00514 (13790) covalent geometry : angle 0.65931 (18790) SS BOND : bond 0.00367 ( 10) SS BOND : angle 0.80812 ( 20) hydrogen bonds : bond 0.05956 ( 777) hydrogen bonds : angle 4.58521 ( 2412) link_NAG-ASN : bond 0.00071 ( 5) link_NAG-ASN : angle 1.97335 ( 15) *********************** 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 339 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 251 time to evaluate : 0.564 Fit side-chains REVERT: A 386 LEU cc_start: 0.7627 (mm) cc_final: 0.7400 (mp) REVERT: A 391 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 181 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: B 270 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7797 (mp) REVERT: C 166 GLU cc_start: 0.7184 (tp30) cc_final: 0.6896 (tt0) REVERT: C 368 ASN cc_start: 0.6039 (OUTLIER) cc_final: 0.5814 (t0) REVERT: C 374 HIS cc_start: 0.7636 (m170) cc_final: 0.7416 (m170) REVERT: D 262 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7666 (t80) REVERT: D 310 LEU cc_start: 0.7653 (mt) cc_final: 0.6917 (pp) REVERT: D 399 MET cc_start: 0.8075 (tpp) cc_final: 0.7724 (tpt) REVERT: E 125 ASN cc_start: 0.7920 (t160) cc_final: 0.7704 (t0) REVERT: E 166 GLU cc_start: 0.7133 (tp30) cc_final: 0.6715 (tt0) REVERT: E 181 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: E 230 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7805 (mm) REVERT: E 262 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7641 (t80) REVERT: E 363 LEU cc_start: 0.6040 (mt) cc_final: 0.5657 (tp) REVERT: E 374 HIS cc_start: 0.7632 (m170) cc_final: 0.7353 (m170) outliers start: 88 outliers final: 51 residues processed: 314 average time/residue: 0.1105 time to fit residues: 51.6928 Evaluate side-chains 313 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 175 THR 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 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 175 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE 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 398 VAL 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 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 365 ASP Chi-restraints excluded: chain C residue 368 ASN 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 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 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 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 107 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098123 restraints weight = 19507.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.101358 restraints weight = 10105.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103456 restraints weight = 6458.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104878 restraints weight = 4763.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105756 restraints weight = 3874.094| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13805 Z= 0.105 Angle : 0.493 8.322 18825 Z= 0.253 Chirality : 0.040 0.145 2290 Planarity : 0.003 0.028 2345 Dihedral : 3.885 24.568 1952 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.38 % Allowed : 25.41 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.21), residues: 1720 helix: 2.98 (0.19), residues: 695 sheet: -0.21 (0.25), residues: 490 loop : -1.08 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 362 TYR 0.012 0.001 TYR D 59 PHE 0.019 0.001 PHE D 387 TRP 0.010 0.001 TRP E 81 HIS 0.002 0.000 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00216 (13790) covalent geometry : angle 0.49284 (18790) SS BOND : bond 0.00168 ( 10) SS BOND : angle 0.41304 ( 20) hydrogen bonds : bond 0.04544 ( 777) hydrogen bonds : angle 4.10582 ( 2412) link_NAG-ASN : bond 0.00071 ( 5) link_NAG-ASN : angle 0.98173 ( 15) *********************** 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 338 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.544 Fit side-chains REVERT: A 295 MET cc_start: 0.8361 (ttp) cc_final: 0.8152 (ttm) REVERT: B 181 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: B 363 LEU cc_start: 0.6196 (mt) cc_final: 0.5781 (tp) REVERT: C 66 THR cc_start: 0.8133 (m) cc_final: 0.7932 (m) REVERT: C 125 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7741 (t0) REVERT: C 166 GLU cc_start: 0.7238 (tp30) cc_final: 0.6902 (tt0) REVERT: D 233 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8067 (tt) REVERT: D 262 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7706 (t80) REVERT: D 285 CYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6615 (m) REVERT: D 310 LEU cc_start: 0.7546 (mt) cc_final: 0.6736 (pp) REVERT: D 374 HIS cc_start: 0.7816 (m170) cc_final: 0.7524 (m170) REVERT: D 399 MET cc_start: 0.8117 (tpp) cc_final: 0.7631 (tpt) REVERT: E 39 MET cc_start: 0.7893 (mmp) cc_final: 0.7485 (mmm) REVERT: E 120 MET cc_start: 0.7818 (tmm) cc_final: 0.7436 (tmm) REVERT: E 166 GLU cc_start: 0.7112 (tp30) cc_final: 0.6686 (tt0) REVERT: E 230 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7827 (mm) REVERT: E 262 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7586 (t80) REVERT: E 363 LEU cc_start: 0.6016 (mt) cc_final: 0.5590 (tp) REVERT: E 374 HIS cc_start: 0.7703 (m170) cc_final: 0.7473 (m170) REVERT: E 387 PHE cc_start: 0.7470 (t80) cc_final: 0.7250 (t80) outliers start: 50 outliers final: 31 residues processed: 318 average time/residue: 0.1077 time to fit residues: 50.8661 Evaluate side-chains 310 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 380 LEU 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 262 PHE 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 114 ASN Chi-restraints excluded: chain C residue 125 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 400 LEU 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 285 CYS Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU 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 230 LEU Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.094832 restraints weight = 19882.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097972 restraints weight = 10443.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099921 restraints weight = 6691.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.101420 restraints weight = 4979.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102283 restraints weight = 4009.417| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13805 Z= 0.162 Angle : 0.574 9.531 18825 Z= 0.289 Chirality : 0.042 0.171 2290 Planarity : 0.004 0.027 2345 Dihedral : 4.119 26.122 1952 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.59 % Allowed : 25.07 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.21), residues: 1720 helix: 2.83 (0.19), residues: 685 sheet: -0.25 (0.25), residues: 480 loop : -1.16 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 354 TYR 0.008 0.001 TYR E 130 PHE 0.025 0.002 PHE D 387 TRP 0.009 0.001 TRP C 81 HIS 0.002 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00370 (13790) covalent geometry : angle 0.57316 (18790) SS BOND : bond 0.00302 ( 10) SS BOND : angle 0.59788 ( 20) hydrogen bonds : bond 0.05174 ( 777) hydrogen bonds : angle 4.25378 ( 2412) link_NAG-ASN : bond 0.00033 ( 5) link_NAG-ASN : angle 1.44378 ( 15) *********************** 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 340 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 272 time to evaluate : 0.523 Fit side-chains REVERT: A 386 LEU cc_start: 0.7560 (mm) cc_final: 0.7339 (mp) REVERT: A 391 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 181 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: C 125 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7751 (t0) REVERT: C 166 GLU cc_start: 0.7180 (tp30) cc_final: 0.6862 (tt0) REVERT: C 262 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7707 (t80) REVERT: D 233 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8000 (tt) REVERT: D 262 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7592 (t80) REVERT: D 310 LEU cc_start: 0.7630 (mt) cc_final: 0.6987 (pp) REVERT: D 374 HIS cc_start: 0.7779 (m170) cc_final: 0.7473 (m170) REVERT: D 399 MET cc_start: 0.8123 (tpp) cc_final: 0.7696 (tpt) REVERT: E 166 GLU cc_start: 0.7140 (tp30) cc_final: 0.6681 (tt0) REVERT: E 230 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7764 (mm) REVERT: E 262 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7559 (t80) REVERT: E 363 LEU cc_start: 0.5988 (mt) cc_final: 0.5582 (tp) REVERT: E 374 HIS cc_start: 0.7676 (m170) cc_final: 0.7412 (m170) REVERT: E 400 LEU cc_start: 0.7851 (tt) cc_final: 0.7611 (tt) outliers start: 68 outliers final: 52 residues processed: 318 average time/residue: 0.1059 time to fit residues: 50.2594 Evaluate side-chains 327 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 296 LEU 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 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 181 GLN Chi-restraints excluded: chain B residue 262 PHE 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 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 235 ASP Chi-restraints excluded: chain C residue 262 PHE 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 400 LEU Chi-restraints excluded: chain D residue 49 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 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 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 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 299 MET 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 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 136 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.107704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.088421 restraints weight = 20482.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.091391 restraints weight = 10789.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.093222 restraints weight = 6938.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094579 restraints weight = 5197.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.095441 restraints weight = 4222.241| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1910 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= 0.170 Angle : 0.590 10.450 18825 Z= 0.297 Chirality : 0.042 0.173 2290 Planarity : 0.004 0.030 2345 Dihedral : 4.242 27.495 1952 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.42 % Allowed : 23.92 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.21), residues: 1720 helix: 2.69 (0.19), residues: 680 sheet: -0.37 (0.25), residues: 480 loop : -1.26 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 354 TYR 0.009 0.001 TYR E 130 PHE 0.027 0.002 PHE D 387 TRP 0.010 0.001 TRP C 81 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00390 (13790) covalent geometry : angle 0.58856 (18790) SS BOND : bond 0.00311 ( 10) SS BOND : angle 0.65296 ( 20) hydrogen bonds : bond 0.05358 ( 777) hydrogen bonds : angle 4.32921 ( 2412) link_NAG-ASN : bond 0.00050 ( 5) link_NAG-ASN : angle 1.55241 ( 15) *********************** 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 360 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 265 time to evaluate : 0.515 Fit side-chains REVERT: A 386 LEU cc_start: 0.7521 (mm) cc_final: 0.7302 (mp) REVERT: A 391 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7387 (mp) REVERT: B 181 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: B 270 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7568 (mp) REVERT: C 125 ASN cc_start: 0.7982 (t160) cc_final: 0.7733 (t0) REVERT: C 166 GLU cc_start: 0.7206 (tp30) cc_final: 0.6882 (tt0) REVERT: C 262 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7707 (t80) REVERT: D 233 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7973 (tt) REVERT: D 262 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7545 (t80) REVERT: D 374 HIS cc_start: 0.7757 (m170) cc_final: 0.7467 (m170) REVERT: D 399 MET cc_start: 0.8116 (tpp) cc_final: 0.7684 (tpt) REVERT: E 166 GLU cc_start: 0.7211 (tp30) cc_final: 0.6693 (tt0) REVERT: E 230 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7758 (mm) REVERT: E 262 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7557 (t80) REVERT: E 363 LEU cc_start: 0.6001 (mt) cc_final: 0.5611 (tp) REVERT: E 368 ASN cc_start: 0.7070 (t0) cc_final: 0.6843 (t0) REVERT: E 371 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6058 (mp0) REVERT: E 374 HIS cc_start: 0.7672 (m170) cc_final: 0.7421 (m170) REVERT: E 400 LEU cc_start: 0.7726 (tt) cc_final: 0.7475 (tt) outliers start: 95 outliers final: 68 residues processed: 337 average time/residue: 0.1035 time to fit residues: 52.4868 Evaluate side-chains 337 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 261 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 363 LEU 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 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 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 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 174 VAL Chi-restraints excluded: chain C residue 175 THR 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 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 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 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 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 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 380 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 48 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098243 restraints weight = 19215.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101337 restraints weight = 10251.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103381 restraints weight = 6677.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104724 restraints weight = 5002.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105480 restraints weight = 4110.546| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13805 Z= 0.111 Angle : 0.518 11.637 18825 Z= 0.262 Chirality : 0.040 0.156 2290 Planarity : 0.003 0.029 2345 Dihedral : 3.914 23.664 1952 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.99 % Allowed : 26.69 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1720 helix: 3.01 (0.19), residues: 690 sheet: -0.21 (0.25), residues: 480 loop : -1.11 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 362 TYR 0.008 0.001 TYR A 95 PHE 0.024 0.001 PHE D 387 TRP 0.010 0.001 TRP A 81 HIS 0.002 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00238 (13790) covalent geometry : angle 0.51701 (18790) SS BOND : bond 0.00456 ( 10) SS BOND : angle 0.84527 ( 20) hydrogen bonds : bond 0.04658 ( 777) hydrogen bonds : angle 4.11224 ( 2412) link_NAG-ASN : bond 0.00047 ( 5) link_NAG-ASN : angle 1.06853 ( 15) *********************** 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 342 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.476 Fit side-chains REVERT: A 386 LEU cc_start: 0.7618 (mm) cc_final: 0.7388 (mp) REVERT: B 181 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: B 270 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7324 (mp) REVERT: B 363 LEU cc_start: 0.6320 (mt) cc_final: 0.5896 (tp) REVERT: C 125 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7645 (t0) REVERT: D 233 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8103 (tt) REVERT: D 310 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7146 (mt) REVERT: D 374 HIS cc_start: 0.7777 (m170) cc_final: 0.7515 (m170) REVERT: D 399 MET cc_start: 0.8164 (tpp) cc_final: 0.7571 (tpt) REVERT: E 166 GLU cc_start: 0.7189 (tp30) cc_final: 0.6774 (tt0) REVERT: E 230 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7900 (mm) REVERT: E 262 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7600 (t80) REVERT: E 362 ARG cc_start: 0.5717 (mtp-110) cc_final: 0.5157 (ptm-80) REVERT: E 363 LEU cc_start: 0.5992 (mt) cc_final: 0.5565 (tp) REVERT: E 374 HIS cc_start: 0.7601 (m170) cc_final: 0.7379 (m170) REVERT: E 387 PHE cc_start: 0.7905 (t80) cc_final: 0.7559 (t80) outliers start: 59 outliers final: 45 residues processed: 318 average time/residue: 0.1036 time to fit residues: 49.2767 Evaluate side-chains 324 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 296 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 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 262 PHE Chi-restraints excluded: chain B residue 270 LEU 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 90 THR Chi-restraints excluded: chain C residue 114 ASN 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 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 400 LEU Chi-restraints excluded: chain D residue 72 ASN 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 299 MET Chi-restraints excluded: chain D residue 310 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 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 380 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094978 restraints weight = 19855.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098042 restraints weight = 10471.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100083 restraints weight = 6745.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101410 restraints weight = 4974.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102298 restraints weight = 4064.219| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2033 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= 0.152 Angle : 0.580 11.613 18825 Z= 0.290 Chirality : 0.042 0.164 2290 Planarity : 0.003 0.032 2345 Dihedral : 4.045 18.521 1950 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.74 % Allowed : 25.41 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.21), residues: 1720 helix: 2.90 (0.19), residues: 680 sheet: -0.24 (0.25), residues: 480 loop : -1.17 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 362 TYR 0.009 0.001 TYR A 95 PHE 0.015 0.002 PHE B 359 TRP 0.009 0.001 TRP C 81 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00346 (13790) covalent geometry : angle 0.57871 (18790) SS BOND : bond 0.00243 ( 10) SS BOND : angle 0.91662 ( 20) hydrogen bonds : bond 0.05114 ( 777) hydrogen bonds : angle 4.23422 ( 2412) link_NAG-ASN : bond 0.00027 ( 5) link_NAG-ASN : angle 1.42073 ( 15) *********************** 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 357 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 272 time to evaluate : 0.540 Fit side-chains REVERT: A 386 LEU cc_start: 0.7552 (mm) cc_final: 0.7322 (mp) REVERT: B 181 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: B 224 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7347 (mp) REVERT: B 270 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7522 (mp) REVERT: B 362 ARG cc_start: 0.5482 (mtp-110) cc_final: 0.5191 (ttp80) REVERT: C 125 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7682 (t0) REVERT: C 236 PHE cc_start: 0.7538 (m-10) cc_final: 0.7312 (m-10) REVERT: C 262 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7644 (t80) REVERT: D 39 MET cc_start: 0.8289 (mmm) cc_final: 0.8051 (mmp) REVERT: D 310 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7292 (mt) REVERT: D 374 HIS cc_start: 0.7767 (m170) cc_final: 0.7490 (m170) REVERT: D 399 MET cc_start: 0.8137 (tpp) cc_final: 0.7610 (tpt) REVERT: E 166 GLU cc_start: 0.7240 (tp30) cc_final: 0.6743 (tt0) REVERT: E 170 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7696 (p) REVERT: E 230 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7748 (mm) REVERT: E 262 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7633 (t80) REVERT: E 310 LEU cc_start: 0.7538 (mt) cc_final: 0.6499 (pp) REVERT: E 363 LEU cc_start: 0.6021 (mt) cc_final: 0.5666 (tp) REVERT: E 371 GLU cc_start: 0.6574 (tm-30) cc_final: 0.5879 (mp0) REVERT: E 374 HIS cc_start: 0.7649 (m170) cc_final: 0.7399 (m170) outliers start: 85 outliers final: 66 residues processed: 330 average time/residue: 0.1044 time to fit residues: 51.6296 Evaluate side-chains 335 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 296 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 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 174 VAL 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 262 PHE Chi-restraints excluded: chain B residue 270 LEU 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 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 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 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 102 VAL 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 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 310 LEU 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 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 380 LEU Chi-restraints excluded: chain E residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 160 optimal weight: 0.0170 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 44 optimal weight: 0.0170 chunk 167 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098246 restraints weight = 19401.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101328 restraints weight = 10328.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103380 restraints weight = 6742.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104556 restraints weight = 5026.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105422 restraints weight = 4198.123| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13805 Z= 0.119 Angle : 0.539 11.394 18825 Z= 0.269 Chirality : 0.041 0.155 2290 Planarity : 0.003 0.034 2345 Dihedral : 3.883 17.656 1950 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.41 % Allowed : 26.35 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1720 helix: 2.97 (0.19), residues: 690 sheet: -0.19 (0.25), residues: 480 loop : -1.09 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 362 TYR 0.008 0.001 TYR A 95 PHE 0.024 0.001 PHE D 387 TRP 0.010 0.001 TRP A 81 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00262 (13790) covalent geometry : angle 0.53820 (18790) SS BOND : bond 0.00297 ( 10) SS BOND : angle 0.85445 ( 20) hydrogen bonds : bond 0.04721 ( 777) hydrogen bonds : angle 4.12123 ( 2412) link_NAG-ASN : bond 0.00034 ( 5) link_NAG-ASN : angle 1.14118 ( 15) *********************** 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 358 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 278 time to evaluate : 0.535 Fit side-chains REVERT: A 386 LEU cc_start: 0.7586 (mm) cc_final: 0.7357 (mp) REVERT: B 181 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: B 224 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 270 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7350 (mp) REVERT: B 362 ARG cc_start: 0.5586 (mtp-110) cc_final: 0.5280 (ttp80) REVERT: B 363 LEU cc_start: 0.6426 (mt) cc_final: 0.5967 (tp) REVERT: C 125 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7657 (t0) REVERT: D 233 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8138 (tt) REVERT: D 310 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7179 (mt) REVERT: D 371 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6175 (mp0) REVERT: D 399 MET cc_start: 0.8173 (tpp) cc_final: 0.7574 (tpt) REVERT: E 166 GLU cc_start: 0.7224 (tp30) cc_final: 0.6807 (tt0) REVERT: E 170 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7699 (p) REVERT: E 230 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7898 (mm) REVERT: E 262 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7633 (t80) REVERT: E 310 LEU cc_start: 0.7436 (mt) cc_final: 0.7095 (mt) REVERT: E 362 ARG cc_start: 0.5738 (mtp-110) cc_final: 0.5178 (ptm-80) REVERT: E 363 LEU cc_start: 0.6039 (mt) cc_final: 0.5628 (tp) REVERT: E 371 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6037 (mp0) REVERT: E 374 HIS cc_start: 0.7641 (m170) cc_final: 0.7412 (m170) outliers start: 80 outliers final: 61 residues processed: 332 average time/residue: 0.1037 time to fit residues: 51.7440 Evaluate side-chains 344 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 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 296 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL 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 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 174 VAL 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 299 MET 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 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 262 PHE Chi-restraints excluded: chain C residue 298 SER 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 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 299 MET Chi-restraints excluded: chain D residue 310 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 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 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 C 249 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100878 restraints weight = 19205.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103940 restraints weight = 10175.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106030 restraints weight = 6643.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107332 restraints weight = 4959.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108227 restraints weight = 4088.969| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13805 Z= 0.112 Angle : 0.535 12.888 18825 Z= 0.267 Chirality : 0.041 0.161 2290 Planarity : 0.003 0.032 2345 Dihedral : 3.780 16.410 1950 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.86 % Allowed : 27.09 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.21), residues: 1720 helix: 3.04 (0.19), residues: 690 sheet: -0.07 (0.26), residues: 435 loop : -1.30 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 362 TYR 0.009 0.001 TYR A 95 PHE 0.034 0.001 PHE D 387 TRP 0.010 0.001 TRP A 81 HIS 0.002 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00243 (13790) covalent geometry : angle 0.53365 (18790) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.80070 ( 20) hydrogen bonds : bond 0.04518 ( 777) hydrogen bonds : angle 4.06429 ( 2412) link_NAG-ASN : bond 0.00049 ( 5) link_NAG-ASN : angle 1.04593 ( 15) ********************** 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 353 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 281 time to evaluate : 0.513 Fit side-chains REVERT: A 386 LEU cc_start: 0.7596 (mm) cc_final: 0.7351 (mp) REVERT: B 181 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6735 (tt0) REVERT: B 224 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7356 (mp) REVERT: B 270 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 362 ARG cc_start: 0.5664 (mtp-110) cc_final: 0.5295 (ttp80) REVERT: B 363 LEU cc_start: 0.6330 (mt) cc_final: 0.5931 (tp) REVERT: C 125 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7637 (t0) REVERT: D 39 MET cc_start: 0.8079 (mmm) cc_final: 0.7781 (mmp) REVERT: D 233 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8113 (tt) REVERT: D 310 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7158 (mt) REVERT: D 399 MET cc_start: 0.8214 (tpp) cc_final: 0.7565 (tpt) REVERT: E 166 GLU cc_start: 0.7229 (tp30) cc_final: 0.6976 (tt0) REVERT: E 170 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7733 (p) REVERT: E 230 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7896 (mm) REVERT: E 262 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7657 (t80) REVERT: E 362 ARG cc_start: 0.5766 (mtp-110) cc_final: 0.4659 (mtt90) REVERT: E 363 LEU cc_start: 0.6013 (mt) cc_final: 0.5678 (tp) REVERT: E 374 HIS cc_start: 0.7636 (m170) cc_final: 0.7416 (m170) outliers start: 72 outliers final: 54 residues processed: 329 average time/residue: 0.1065 time to fit residues: 52.6513 Evaluate side-chains 336 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL 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 174 VAL 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 299 MET 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 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 262 PHE Chi-restraints excluded: chain C residue 298 SER 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 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 299 MET Chi-restraints excluded: chain D residue 310 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 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 299 MET Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 C 32 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098153 restraints weight = 19582.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101312 restraints weight = 10110.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103434 restraints weight = 6461.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104682 restraints weight = 4762.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105660 restraints weight = 3924.644| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13805 Z= 0.164 Angle : 0.606 12.695 18825 Z= 0.301 Chirality : 0.043 0.172 2290 Planarity : 0.004 0.034 2345 Dihedral : 4.072 16.650 1950 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.47 % Allowed : 26.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.21), residues: 1720 helix: 2.63 (0.19), residues: 695 sheet: -0.27 (0.25), residues: 480 loop : -1.07 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 354 TYR 0.010 0.001 TYR A 95 PHE 0.030 0.002 PHE D 387 TRP 0.009 0.001 TRP C 81 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00377 (13790) covalent geometry : angle 0.60438 (18790) SS BOND : bond 0.00282 ( 10) SS BOND : angle 0.94337 ( 20) hydrogen bonds : bond 0.05171 ( 777) hydrogen bonds : angle 4.27487 ( 2412) link_NAG-ASN : bond 0.00049 ( 5) link_NAG-ASN : angle 1.54454 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.59 seconds wall clock time: 36 minutes 6.75 seconds (2166.75 seconds total)