Starting phenix.real_space_refine on Sat Sep 12 19:43:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.map" model { file = "/net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xit_22200/09_2026/6xit_22200.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9500 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 12 5.49 5 S 52 5.16 5 C 6704 2.51 5 N 1688 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10403 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 3, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10403 At special positions: 0 Unit cell: (87, 87, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 52 16.00 P 12 15.00 O 1944 8.00 N 1688 7.00 C 6704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 166 " distance=2.04 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 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 303.4 milliseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 35.2% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.834A pdb=" N LEU A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 90 through 121 removed outlier: 3.612A pdb=" N TYR A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 117 " --> pdb=" O TRP A 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 118 " --> pdb=" O TRP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.549A pdb=" N SER A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 196 removed outlier: 3.974A pdb=" N ILE A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 removed outlier: 3.834A pdb=" N LYS A 200 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA A 202 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 removed outlier: 4.512A pdb=" N HIS A 357 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.516A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.834A pdb=" N LEU B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 90 through 121 removed outlier: 3.612A pdb=" N TYR B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 117 " --> pdb=" O TRP B 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 118 " --> pdb=" O TRP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 153 removed outlier: 3.549A pdb=" N SER B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 196 removed outlier: 3.974A pdb=" N ILE B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.835A pdb=" N LYS B 200 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 4.512A pdb=" N HIS B 357 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.515A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 381 " --> pdb=" O ASN B 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 81 removed outlier: 3.834A pdb=" N LEU C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 90 through 121 removed outlier: 3.612A pdb=" N TYR C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 117 " --> pdb=" O TRP C 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 153 removed outlier: 3.549A pdb=" N SER C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 196 removed outlier: 3.974A pdb=" N ILE C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS C 190 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.834A pdb=" N LYS C 200 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.512A pdb=" N HIS C 357 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 381 removed outlier: 3.517A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.834A pdb=" N LEU D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 90 through 121 removed outlier: 3.613A pdb=" N TYR D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 117 " --> pdb=" O TRP D 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR D 118 " --> pdb=" O TRP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 153 removed outlier: 3.549A pdb=" N SER D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 149 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 196 removed outlier: 3.975A pdb=" N ILE D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 179 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.835A pdb=" N LYS D 200 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 202 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 357 removed outlier: 4.512A pdb=" N HIS D 357 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 381 removed outlier: 3.516A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 removed outlier: 7.034A pdb=" N HIS A 68 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 207 removed outlier: 6.741A pdb=" N ALA A 211 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 254 through 262 removed outlier: 4.974A pdb=" N LYS A 247 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 241 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU A 236 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A 313 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 68 removed outlier: 7.082A pdb=" N HIS B 68 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 207 removed outlier: 6.740A pdb=" N ALA B 211 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 254 through 262 removed outlier: 4.973A pdb=" N LYS B 247 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 241 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU B 236 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET B 313 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 336 through 338 Processing sheet with id=AB3, first strand: chain 'C' and resid 205 through 207 Processing sheet with id=AB4, first strand: chain 'C' and resid 205 through 207 removed outlier: 6.740A pdb=" N ALA C 211 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 262 removed outlier: 4.974A pdb=" N LYS C 247 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA C 241 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU C 236 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 313 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB7, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB8, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AB9, first strand: chain 'D' and resid 205 through 207 removed outlier: 6.741A pdb=" N ALA D 211 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 254 through 262 removed outlier: 4.974A pdb=" N LYS D 247 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU D 236 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET D 313 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 336 through 338 440 hydrogen bonds defined for protein. 1236 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: 1.78 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2004 1.32 - 1.45: 2713 1.45 - 1.57: 5827 1.57 - 1.70: 16 1.70 - 1.82: 80 Bond restraints: 10640 Sorted by residual: bond pdb=" O4 PIO B 401 " pdb=" P4 PIO B 401 " ideal model delta sigma weight residual 1.710 1.585 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O4 PIO C 401 " pdb=" P4 PIO C 401 " ideal model delta sigma weight residual 1.710 1.586 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4 PIO A 401 " pdb=" P4 PIO A 401 " ideal model delta sigma weight residual 1.710 1.602 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" O4 PIO D 401 " pdb=" P4 PIO D 401 " ideal model delta sigma weight residual 1.710 1.603 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O5 PIO C 401 " pdb=" P5 PIO C 401 " ideal model delta sigma weight residual 1.699 1.596 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 10635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 14056 2.24 - 4.49: 392 4.49 - 6.73: 44 6.73 - 8.98: 6 8.98 - 11.22: 6 Bond angle restraints: 14504 Sorted by residual: angle pdb=" C HIS B 69 " pdb=" N GLY B 70 " pdb=" CA GLY B 70 " ideal model delta sigma weight residual 121.41 131.06 -9.65 1.96e+00 2.60e-01 2.42e+01 angle pdb=" C HIS D 69 " pdb=" N GLY D 70 " pdb=" CA GLY D 70 " ideal model delta sigma weight residual 121.41 131.00 -9.59 1.96e+00 2.60e-01 2.39e+01 angle pdb=" C HIS A 69 " pdb=" N GLY A 70 " pdb=" CA GLY A 70 " ideal model delta sigma weight residual 121.41 130.97 -9.56 1.96e+00 2.60e-01 2.38e+01 angle pdb=" C HIS C 69 " pdb=" N GLY C 70 " pdb=" CA GLY C 70 " ideal model delta sigma weight residual 121.41 130.97 -9.56 1.96e+00 2.60e-01 2.38e+01 angle pdb=" N TRP A 91 " pdb=" CA TRP A 91 " pdb=" C TRP A 91 " ideal model delta sigma weight residual 111.36 107.07 4.29 1.09e+00 8.42e-01 1.55e+01 ... (remaining 14499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5516 17.26 - 34.51: 555 34.51 - 51.77: 96 51.77 - 69.03: 9 69.03 - 86.29: 8 Dihedral angle restraints: 6184 sinusoidal: 2360 harmonic: 3824 Sorted by residual: dihedral pdb=" CA TYR C 159 " pdb=" C TYR C 159 " pdb=" N ARG C 160 " pdb=" CA ARG C 160 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TYR A 159 " pdb=" C TYR A 159 " pdb=" N ARG A 160 " pdb=" CA ARG A 160 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR D 159 " pdb=" C TYR D 159 " pdb=" N ARG D 160 " pdb=" CA ARG D 160 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 6181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1319 0.067 - 0.134: 305 0.134 - 0.201: 56 0.201 - 0.268: 4 0.268 - 0.335: 4 Chirality restraints: 1688 Sorted by residual: chirality pdb=" C1 PIO D 401 " pdb=" C2 PIO D 401 " pdb=" C6 PIO D 401 " pdb=" O1 PIO D 401 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1 PIO A 401 " pdb=" C2 PIO A 401 " pdb=" C6 PIO A 401 " pdb=" O1 PIO A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 PIO B 401 " pdb=" C2 PIO B 401 " pdb=" C6 PIO B 401 " pdb=" O1 PIO B 401 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1685 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 299 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO D 300 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 300 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 300 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 299 " -0.036 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO A 300 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 299 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 300 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " -0.030 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 153 2.54 - 3.19: 9222 3.19 - 3.84: 20848 3.84 - 4.49: 28243 4.49 - 5.14: 46141 Nonbonded interactions: 104607 Sorted by model distance: nonbonded pdb=" O52 PIO D 401 " pdb=" O6 PIO D 401 " model vdw 1.894 3.040 nonbonded pdb=" O52 PIO B 401 " pdb=" O6 PIO B 401 " model vdw 1.897 3.040 nonbonded pdb=" O52 PIO C 401 " pdb=" O6 PIO C 401 " model vdw 1.903 3.040 nonbonded pdb=" O12 PIO A 401 " pdb=" O2 PIO A 401 " model vdw 1.935 3.040 nonbonded pdb=" O52 PIO A 401 " pdb=" O6 PIO A 401 " model vdw 1.968 3.040 ... (remaining 104602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 401) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.240 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.125 10644 Z= 0.443 Angle : 0.933 11.219 14512 Z= 0.511 Chirality : 0.060 0.335 1688 Planarity : 0.006 0.054 1788 Dihedral : 14.198 86.285 3708 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.74 % Allowed : 12.87 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.18), residues: 1300 helix: -4.27 (0.10), residues: 408 sheet: -1.49 (0.30), residues: 232 loop : -1.59 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 120 TYR 0.019 0.003 TYR A 360 PHE 0.019 0.002 PHE C 98 TRP 0.014 0.003 TRP C 114 HIS 0.004 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00962 / 0.44 (10640) covalent geometry : angle 0.93199 / 0.51 (14504) SS BOND : bond 0.00732 / 0.34 ( 4) SS BOND : angle 2.19138 / 1.22 ( 8) hydrogen bonds : bond 0.27449 / 17.73 ( 432) hydrogen bonds : angle 9.77054 / 6.93 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.435 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 195 average time/residue: 0.0774 time to fit residues: 23.5150 Evaluate side-chains 135 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain D residue 231 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 176 GLN A 233 HIS A 258 ASN A 286 ASN B 68 HIS B 176 GLN B 233 HIS B 258 ASN B 286 ASN C 68 HIS C 176 GLN C 233 HIS C 258 ASN C 286 ASN C 322 GLN D 68 HIS D 176 GLN D 233 HIS D 258 ASN D 286 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069472 restraints weight = 29902.865| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.56 r_work: 0.3000 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10644 Z= 0.137 Angle : 0.571 6.672 14512 Z= 0.294 Chirality : 0.044 0.141 1688 Planarity : 0.005 0.034 1788 Dihedral : 6.789 58.848 1456 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.67 % Allowed : 17.19 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1300 helix: -1.61 (0.21), residues: 432 sheet: -1.11 (0.30), residues: 236 loop : -0.62 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 120 TYR 0.009 0.001 TYR B 360 PHE 0.009 0.001 PHE A 83 TRP 0.013 0.001 TRP A 114 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10640) covalent geometry : angle 0.57018 / 0.29 (14504) SS BOND : bond 0.00232 / 0.11 ( 4) SS BOND : angle 1.06286 / 0.60 ( 8) hydrogen bonds : bond 0.04171 / 2.66 ( 432) hydrogen bonds : angle 5.05368 / 3.60 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.465 Fit side-chains REVERT: A 311 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6648 (mt-10) REVERT: A 380 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5418 (pm20) REVERT: B 88 ASP cc_start: 0.7482 (p0) cc_final: 0.7265 (p0) REVERT: B 115 LEU cc_start: 0.8029 (mt) cc_final: 0.7757 (tp) REVERT: B 236 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 377 ASN cc_start: 0.7298 (m-40) cc_final: 0.6961 (m-40) REVERT: B 380 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.5366 (pm20) REVERT: C 115 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7753 (tp) REVERT: C 377 ASN cc_start: 0.7370 (m-40) cc_final: 0.7142 (m-40) REVERT: C 380 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5203 (pm20) REVERT: D 115 LEU cc_start: 0.8047 (mt) cc_final: 0.7763 (tp) REVERT: D 377 ASN cc_start: 0.7343 (m-40) cc_final: 0.7102 (m-40) REVERT: D 380 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.5313 (pm20) outliers start: 29 outliers final: 15 residues processed: 228 average time/residue: 0.0720 time to fit residues: 25.7447 Evaluate side-chains 185 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 380 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.077065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067427 restraints weight = 30175.834| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.46 r_work: 0.2959 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10644 Z= 0.268 Angle : 0.661 6.273 14512 Z= 0.342 Chirality : 0.049 0.209 1688 Planarity : 0.005 0.029 1788 Dihedral : 6.770 59.362 1448 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 7.08 % Allowed : 16.45 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1300 helix: -0.36 (0.24), residues: 440 sheet: -0.72 (0.30), residues: 228 loop : -0.18 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 120 TYR 0.014 0.002 TYR C 118 PHE 0.020 0.002 PHE D 98 TRP 0.019 0.002 TRP A 114 HIS 0.005 0.002 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 (10640) covalent geometry : angle 0.66009 / 0.34 (14504) SS BOND : bond 0.00384 / 0.18 ( 4) SS BOND : angle 1.38601 / 0.77 ( 8) hydrogen bonds : bond 0.04242 / 2.70 ( 432) hydrogen bonds : angle 4.98536 / 3.56 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 0.422 Fit side-chains REVERT: A 370 LYS cc_start: 0.8924 (tmmt) cc_final: 0.8703 (ttmm) REVERT: A 380 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.5031 (pm20) REVERT: B 88 ASP cc_start: 0.7605 (p0) cc_final: 0.7359 (p0) REVERT: B 115 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (tp) REVERT: B 377 ASN cc_start: 0.7338 (m-40) cc_final: 0.6751 (m-40) REVERT: C 115 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7795 (tp) REVERT: C 370 LYS cc_start: 0.8922 (tmmt) cc_final: 0.8670 (ttmm) REVERT: C 377 ASN cc_start: 0.7454 (m-40) cc_final: 0.6957 (m-40) REVERT: D 115 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7804 (tp) REVERT: D 370 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8668 (ttmm) REVERT: D 377 ASN cc_start: 0.7402 (m-40) cc_final: 0.7140 (m-40) REVERT: D 380 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.5261 (pm20) outliers start: 77 outliers final: 57 residues processed: 212 average time/residue: 0.0816 time to fit residues: 26.5259 Evaluate side-chains 218 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 156 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 380 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 66 ASN B 94 ASN C 66 ASN C 94 ASN D 66 ASN D 94 ASN D 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067933 restraints weight = 30094.981| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.50 r_work: 0.2975 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10644 Z= 0.209 Angle : 0.579 5.469 14512 Z= 0.300 Chirality : 0.047 0.211 1688 Planarity : 0.004 0.027 1788 Dihedral : 6.611 57.391 1448 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.89 % Allowed : 17.92 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1300 helix: 0.04 (0.25), residues: 440 sheet: -0.65 (0.31), residues: 236 loop : -0.06 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 120 TYR 0.011 0.002 TYR B 360 PHE 0.014 0.002 PHE D 109 TRP 0.015 0.002 TRP A 114 HIS 0.004 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (10640) covalent geometry : angle 0.57873 / 0.30 (14504) SS BOND : bond 0.00267 / 0.13 ( 4) SS BOND : angle 1.35033 / 0.75 ( 8) hydrogen bonds : bond 0.03761 / 2.40 ( 432) hydrogen bonds : angle 4.80098 / 3.43 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 0.415 Fit side-chains REVERT: B 88 ASP cc_start: 0.7645 (p0) cc_final: 0.7317 (p0) REVERT: B 115 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7827 (tp) REVERT: B 187 MET cc_start: 0.8394 (mmp) cc_final: 0.7829 (mmp) REVERT: B 236 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 377 ASN cc_start: 0.7355 (m-40) cc_final: 0.7062 (m-40) REVERT: C 115 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7856 (tp) REVERT: C 377 ASN cc_start: 0.7329 (m-40) cc_final: 0.7027 (m-40) REVERT: D 115 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7845 (tp) REVERT: D 187 MET cc_start: 0.8412 (mmp) cc_final: 0.7859 (mmp) REVERT: D 377 ASN cc_start: 0.7366 (m-40) cc_final: 0.6835 (m-40) outliers start: 75 outliers final: 56 residues processed: 204 average time/residue: 0.0770 time to fit residues: 24.5590 Evaluate side-chains 210 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068031 restraints weight = 29533.614| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.38 r_work: 0.2975 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10644 Z= 0.158 Angle : 0.531 5.509 14512 Z= 0.275 Chirality : 0.045 0.193 1688 Planarity : 0.004 0.026 1788 Dihedral : 6.457 54.983 1448 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.25 % Allowed : 18.93 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1300 helix: 0.35 (0.25), residues: 440 sheet: -0.31 (0.32), residues: 228 loop : 0.19 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.010 0.001 TYR D 360 PHE 0.014 0.002 PHE A 98 TRP 0.012 0.001 TRP A 114 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10640) covalent geometry : angle 0.53031 / 0.27 (14504) SS BOND : bond 0.00298 / 0.14 ( 4) SS BOND : angle 1.15457 / 0.65 ( 8) hydrogen bonds : bond 0.03460 / 2.22 ( 432) hydrogen bonds : angle 4.59434 / 3.27 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 283 HIS cc_start: 0.9119 (OUTLIER) cc_final: 0.8558 (t70) REVERT: A 370 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8389 (ttmm) REVERT: A 374 GLU cc_start: 0.8169 (mp0) cc_final: 0.7917 (mp0) REVERT: B 115 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 377 ASN cc_start: 0.7305 (m-40) cc_final: 0.7002 (m-40) REVERT: C 115 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7704 (tp) REVERT: C 236 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7370 (mm-30) REVERT: C 283 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8622 (t70) REVERT: C 370 LYS cc_start: 0.8989 (tmmt) cc_final: 0.8368 (ttmt) REVERT: C 377 ASN cc_start: 0.7351 (m-40) cc_final: 0.7053 (m-40) REVERT: D 115 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7743 (tp) REVERT: D 283 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8602 (t70) REVERT: D 370 LYS cc_start: 0.8985 (tmmt) cc_final: 0.8395 (ttmt) REVERT: D 374 GLU cc_start: 0.8310 (mp0) cc_final: 0.8072 (mp0) REVERT: D 377 ASN cc_start: 0.7389 (m-40) cc_final: 0.7091 (m-40) outliers start: 68 outliers final: 54 residues processed: 210 average time/residue: 0.0774 time to fit residues: 25.3248 Evaluate side-chains 225 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068752 restraints weight = 29838.744| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.45 r_work: 0.2987 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10644 Z= 0.135 Angle : 0.520 6.710 14512 Z= 0.266 Chirality : 0.044 0.190 1688 Planarity : 0.003 0.026 1788 Dihedral : 6.362 55.295 1448 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.97 % Allowed : 20.31 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1300 helix: 0.55 (0.25), residues: 440 sheet: -0.21 (0.32), residues: 228 loop : 0.30 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.009 0.001 TYR D 360 PHE 0.009 0.001 PHE A 83 TRP 0.010 0.001 TRP A 114 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10640) covalent geometry : angle 0.51980 / 0.27 (14504) SS BOND : bond 0.00327 / 0.15 ( 4) SS BOND : angle 1.07313 / 0.60 ( 8) hydrogen bonds : bond 0.03275 / 2.12 ( 432) hydrogen bonds : angle 4.43724 / 3.15 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7429 (mm-30) REVERT: A 271 ASP cc_start: 0.8307 (p0) cc_final: 0.8081 (p0) REVERT: A 283 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.8473 (t70) REVERT: A 370 LYS cc_start: 0.9004 (tmmt) cc_final: 0.8304 (ttmt) REVERT: B 115 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7698 (tp) REVERT: B 377 ASN cc_start: 0.7272 (m-40) cc_final: 0.6984 (m-40) REVERT: C 115 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7654 (tp) REVERT: C 283 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8565 (t70) REVERT: C 311 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: C 377 ASN cc_start: 0.7384 (m-40) cc_final: 0.7073 (m-40) REVERT: D 115 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7686 (tp) REVERT: D 283 HIS cc_start: 0.9134 (OUTLIER) cc_final: 0.8560 (t70) REVERT: D 370 LYS cc_start: 0.8978 (tmmt) cc_final: 0.8273 (ttmm) REVERT: D 374 GLU cc_start: 0.8337 (mp0) cc_final: 0.8029 (mp0) REVERT: D 377 ASN cc_start: 0.7293 (m-40) cc_final: 0.7016 (m-40) outliers start: 65 outliers final: 54 residues processed: 215 average time/residue: 0.0815 time to fit residues: 27.0434 Evaluate side-chains 232 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067924 restraints weight = 29688.900| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.43 r_work: 0.2967 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10644 Z= 0.179 Angle : 0.554 7.129 14512 Z= 0.286 Chirality : 0.045 0.183 1688 Planarity : 0.004 0.026 1788 Dihedral : 6.374 53.533 1448 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.89 % Allowed : 19.76 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1300 helix: 0.52 (0.25), residues: 440 sheet: -0.12 (0.32), residues: 228 loop : 0.32 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.010 0.001 TYR D 360 PHE 0.012 0.001 PHE D 109 TRP 0.014 0.001 TRP A 114 HIS 0.003 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10640) covalent geometry : angle 0.55376 / 0.29 (14504) SS BOND : bond 0.00265 / 0.13 ( 4) SS BOND : angle 1.13085 / 0.63 ( 8) hydrogen bonds : bond 0.03437 / 2.20 ( 432) hydrogen bonds : angle 4.53039 / 3.22 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 170 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 271 ASP cc_start: 0.8345 (p0) cc_final: 0.8116 (p0) REVERT: A 283 HIS cc_start: 0.9148 (OUTLIER) cc_final: 0.8576 (t70) REVERT: B 115 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 187 MET cc_start: 0.8282 (mmp) cc_final: 0.7966 (mmp) REVERT: B 377 ASN cc_start: 0.7231 (m-40) cc_final: 0.6924 (m-40) REVERT: C 115 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7741 (tp) REVERT: C 187 MET cc_start: 0.8289 (mmp) cc_final: 0.7941 (mmp) REVERT: C 236 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 283 HIS cc_start: 0.9147 (OUTLIER) cc_final: 0.8600 (t70) REVERT: C 311 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: C 377 ASN cc_start: 0.7370 (m-40) cc_final: 0.7059 (m-40) REVERT: D 115 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7664 (tp) REVERT: D 187 MET cc_start: 0.8321 (mmp) cc_final: 0.8004 (mmp) REVERT: D 283 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8591 (t70) REVERT: D 370 LYS cc_start: 0.8993 (tmmt) cc_final: 0.8719 (ttmm) REVERT: D 377 ASN cc_start: 0.7377 (m-40) cc_final: 0.7061 (m-40) outliers start: 75 outliers final: 60 residues processed: 209 average time/residue: 0.0800 time to fit residues: 26.0860 Evaluate side-chains 230 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 163 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.078932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069039 restraints weight = 29400.207| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.44 r_work: 0.2998 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10644 Z= 0.124 Angle : 0.505 5.858 14512 Z= 0.262 Chirality : 0.044 0.136 1688 Planarity : 0.003 0.026 1788 Dihedral : 6.269 55.414 1448 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.43 % Allowed : 20.13 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1300 helix: 0.65 (0.26), residues: 440 sheet: -0.00 (0.32), residues: 228 loop : 0.40 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 378 TYR 0.009 0.001 TYR D 360 PHE 0.008 0.001 PHE A 83 TRP 0.008 0.001 TRP A 114 HIS 0.002 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10640) covalent geometry : angle 0.50417 / 0.26 (14504) SS BOND : bond 0.00306 / 0.14 ( 4) SS BOND : angle 1.01956 / 0.57 ( 8) hydrogen bonds : bond 0.03154 / 2.05 ( 432) hydrogen bonds : angle 4.36122 / 3.10 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7538 (tp) REVERT: A 231 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 236 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 283 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8574 (t70) REVERT: B 187 MET cc_start: 0.8258 (mmp) cc_final: 0.7973 (mmp) REVERT: B 236 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 377 ASN cc_start: 0.7122 (m-40) cc_final: 0.6818 (m-40) REVERT: C 115 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7709 (tp) REVERT: C 187 MET cc_start: 0.8245 (mmp) cc_final: 0.7937 (mmp) REVERT: C 271 ASP cc_start: 0.8254 (p0) cc_final: 0.8041 (p0) REVERT: C 283 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8506 (t70) REVERT: C 311 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: C 377 ASN cc_start: 0.7387 (m-40) cc_final: 0.7079 (m-40) REVERT: D 187 MET cc_start: 0.8269 (mmp) cc_final: 0.7988 (mmp) REVERT: D 283 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8507 (t70) REVERT: D 377 ASN cc_start: 0.7335 (m-40) cc_final: 0.7032 (m-40) outliers start: 70 outliers final: 53 residues processed: 208 average time/residue: 0.0771 time to fit residues: 25.1684 Evaluate side-chains 232 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068650 restraints weight = 29455.246| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.39 r_work: 0.2990 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10644 Z= 0.146 Angle : 0.523 7.197 14512 Z= 0.269 Chirality : 0.044 0.166 1688 Planarity : 0.003 0.026 1788 Dihedral : 6.261 54.083 1448 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.53 % Allowed : 20.50 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1300 helix: 0.67 (0.25), residues: 440 sheet: 0.05 (0.32), residues: 228 loop : 0.41 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 120 TYR 0.009 0.001 TYR D 360 PHE 0.009 0.001 PHE A 109 TRP 0.011 0.001 TRP A 114 HIS 0.002 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10640) covalent geometry : angle 0.52220 / 0.27 (14504) SS BOND : bond 0.00290 / 0.14 ( 4) SS BOND : angle 0.98875 / 0.55 ( 8) hydrogen bonds : bond 0.03281 / 2.12 ( 432) hydrogen bonds : angle 4.37483 / 3.11 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 174 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.8277 (mmp) cc_final: 0.7998 (mmp) REVERT: A 231 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7527 (p0) REVERT: A 236 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7292 (mm-30) REVERT: A 271 ASP cc_start: 0.8317 (p0) cc_final: 0.8084 (p0) REVERT: A 283 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8521 (t70) REVERT: B 187 MET cc_start: 0.8243 (mmp) cc_final: 0.7971 (mmp) REVERT: B 236 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7429 (mm-30) REVERT: B 377 ASN cc_start: 0.7130 (m-40) cc_final: 0.6830 (m-40) REVERT: C 115 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7758 (tp) REVERT: C 187 MET cc_start: 0.8260 (mmp) cc_final: 0.7966 (mmp) REVERT: C 271 ASP cc_start: 0.8279 (p0) cc_final: 0.8057 (p0) REVERT: C 283 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8529 (t70) REVERT: C 311 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: C 377 ASN cc_start: 0.7370 (m-40) cc_final: 0.7091 (m-40) REVERT: D 115 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7649 (tp) REVERT: D 187 MET cc_start: 0.8279 (mmp) cc_final: 0.8006 (mmp) REVERT: D 283 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8523 (t70) REVERT: D 377 ASN cc_start: 0.7355 (m-40) cc_final: 0.7049 (m-40) outliers start: 71 outliers final: 57 residues processed: 207 average time/residue: 0.0708 time to fit residues: 23.2989 Evaluate side-chains 230 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 5 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069574 restraints weight = 29229.524| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.39 r_work: 0.3011 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10644 Z= 0.113 Angle : 0.501 7.120 14512 Z= 0.259 Chirality : 0.043 0.138 1688 Planarity : 0.003 0.025 1788 Dihedral : 6.191 55.699 1448 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.33 % Allowed : 22.24 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1300 helix: 0.74 (0.26), residues: 440 sheet: -0.01 (0.32), residues: 240 loop : 0.52 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 378 TYR 0.008 0.001 TYR D 360 PHE 0.010 0.001 PHE B 93 TRP 0.006 0.001 TRP A 114 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10640) covalent geometry : angle 0.50052 / 0.26 (14504) SS BOND : bond 0.00333 / 0.15 ( 4) SS BOND : angle 1.01259 / 0.57 ( 8) hydrogen bonds : bond 0.03076 / 2.01 ( 432) hydrogen bonds : angle 4.24722 / 3.01 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.8250 (mmp) cc_final: 0.7963 (mmp) REVERT: A 283 HIS cc_start: 0.9045 (OUTLIER) cc_final: 0.8508 (t70) REVERT: B 187 MET cc_start: 0.8226 (mmp) cc_final: 0.7965 (mmp) REVERT: B 236 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 377 ASN cc_start: 0.7159 (m-40) cc_final: 0.6854 (m-40) REVERT: C 115 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7687 (tp) REVERT: C 187 MET cc_start: 0.8211 (mmp) cc_final: 0.7946 (mmp) REVERT: C 283 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8468 (t70) REVERT: D 115 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7646 (tp) REVERT: D 187 MET cc_start: 0.8217 (mmp) cc_final: 0.7953 (mmp) REVERT: D 283 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8492 (t70) REVERT: D 377 ASN cc_start: 0.7373 (m-40) cc_final: 0.7069 (m-40) outliers start: 58 outliers final: 46 residues processed: 201 average time/residue: 0.0721 time to fit residues: 22.9961 Evaluate side-chains 216 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 321 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.078990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069385 restraints weight = 29514.571| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.36 r_work: 0.3005 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10644 Z= 0.133 Angle : 0.514 8.013 14512 Z= 0.265 Chirality : 0.044 0.143 1688 Planarity : 0.003 0.025 1788 Dihedral : 6.199 54.548 1448 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.97 % Allowed : 22.15 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1300 helix: 0.70 (0.26), residues: 440 sheet: 0.08 (0.33), residues: 232 loop : 0.48 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 120 TYR 0.008 0.001 TYR D 360 PHE 0.008 0.001 PHE B 93 TRP 0.009 0.001 TRP A 114 HIS 0.003 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10640) covalent geometry : angle 0.51336 / 0.26 (14504) SS BOND : bond 0.00309 / 0.14 ( 4) SS BOND : angle 0.96973 / 0.54 ( 8) hydrogen bonds : bond 0.03147 / 2.04 ( 432) hydrogen bonds : angle 4.27017 / 3.03 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.37 seconds wall clock time: 35 minutes 54.39 seconds (2154.39 seconds total)