Starting phenix.real_space_refine on Thu Sep 18 05:01:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh9_19173/09_2025/8rh9_19173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh9_19173/09_2025/8rh9_19173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rh9_19173/09_2025/8rh9_19173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh9_19173/09_2025/8rh9_19173.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rh9_19173/09_2025/8rh9_19173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh9_19173/09_2025/8rh9_19173.map" } resolution = 3.21 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 Cl 1 4.86 5 C 9383 2.51 5 N 2230 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14247 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2750 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2750 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2750 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2750 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2750 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 102 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 1, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 98 Unusual residues: {' CL': 1, 'A8W': 1, 'HEX': 3, 'NAG': 2, 'OCT': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {'D10': 1, 'HEX': 3, 'NAG': 2, 'OCT': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {'D10': 1, 'D12': 1, 'HEX': 4, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {'D10': 3, 'HEX': 2, 'NAG': 2, 'OCT': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 4.14, per 1000 atoms: 0.29 Number of scatterers: 14247 At special positions: 0 Unit cell: (93.4775, 93.4775, 135.173, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 76 16.00 O 2557 8.00 N 2230 7.00 C 9383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 502 " - " ASN B 140 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 667.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 40.8% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 146 through 153 removed outlier: 4.163A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.940A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.903A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 312 Processing helix chain 'A' and resid 313 through 335 removed outlier: 3.681A pdb=" N GLY A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 377 removed outlier: 3.544A pdb=" N ILE A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 3.841A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.898A pdb=" N LEU B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 79' Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 146 through 153 removed outlier: 4.085A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.932A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.982A pdb=" N SER B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 312 Processing helix chain 'B' and resid 313 through 335 removed outlier: 3.608A pdb=" N GLY B 317 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 377 removed outlier: 3.687A pdb=" N TYR B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 3.900A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.876A pdb=" N LEU C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 146 through 153 removed outlier: 3.513A pdb=" N LEU C 149 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.939A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.877A pdb=" N SER C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 312 Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.582A pdb=" N GLY C 317 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 377 removed outlier: 3.554A pdb=" N ILE C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 353 " --> pdb=" O TRP C 349 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 3.901A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 146 through 153 removed outlier: 4.207A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 280 through 302 removed outlier: 3.960A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.841A pdb=" N SER D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 313 through 335 removed outlier: 3.597A pdb=" N GLY D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 377 removed outlier: 3.697A pdb=" N TYR D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 3.972A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 146 through 153 removed outlier: 4.001A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 280 through 302 removed outlier: 3.945A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.991A pdb=" N SER E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 312 Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.616A pdb=" N VAL E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 377 removed outlier: 3.624A pdb=" N ILE E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 3.970A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.606A pdb=" N TRP A 128 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.000A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP A 128 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.834A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 256 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 3.597A pdb=" N TRP B 128 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.967A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 128 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 160 removed outlier: 4.560A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.639A pdb=" N TRP C 128 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.974A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP C 128 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.838A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 210 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 256 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.598A pdb=" N TRP D 128 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 7.082A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP D 128 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.816A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D 210 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 145 removed outlier: 3.564A pdb=" N MET E 143 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP E 128 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.951A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP E 128 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.829A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 210 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 256 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3240 1.33 - 1.45: 3228 1.45 - 1.57: 7960 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14568 Sorted by residual: bond pdb=" N ASN E 140 " pdb=" CA ASN E 140 " ideal model delta sigma weight residual 1.457 1.505 -0.048 1.16e-02 7.43e+03 1.71e+01 bond pdb=" N ASN B 140 " pdb=" CA ASN B 140 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.16e-02 7.43e+03 1.64e+01 bond pdb=" N ASN A 140 " pdb=" CA ASN A 140 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.16e-02 7.43e+03 1.45e+01 bond pdb=" O1 A8W B 509 " pdb=" S A8W B 509 " ideal model delta sigma weight residual 1.636 1.564 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N ASN C 140 " pdb=" CA ASN C 140 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.16e-02 7.43e+03 1.24e+01 ... (remaining 14563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 19159 1.64 - 3.29: 292 3.29 - 4.93: 217 4.93 - 6.58: 2 6.58 - 8.22: 3 Bond angle restraints: 19673 Sorted by residual: angle pdb=" C ASN B 140 " pdb=" CA ASN B 140 " pdb=" CB ASN B 140 " ideal model delta sigma weight residual 111.02 104.96 6.06 1.61e+00 3.86e-01 1.42e+01 angle pdb=" N ASN B 140 " pdb=" CA ASN B 140 " pdb=" C ASN B 140 " ideal model delta sigma weight residual 112.59 116.07 -3.48 1.22e+00 6.72e-01 8.14e+00 angle pdb=" O ASN E 139 " pdb=" C ASN E 139 " pdb=" N ASN E 140 " ideal model delta sigma weight residual 122.73 119.13 3.60 1.29e+00 6.01e-01 7.79e+00 angle pdb=" CA ASN E 139 " pdb=" C ASN E 139 " pdb=" N ASN E 140 " ideal model delta sigma weight residual 116.08 119.65 -3.57 1.29e+00 6.01e-01 7.65e+00 angle pdb=" O2 A8W B 509 " pdb=" S A8W B 509 " pdb=" O4 A8W B 509 " ideal model delta sigma weight residual 114.46 106.24 8.22 3.00e+00 1.11e-01 7.51e+00 ... (remaining 19668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.72: 8689 30.72 - 61.43: 70 61.43 - 92.15: 2 92.15 - 122.86: 0 122.86 - 153.58: 2 Dihedral angle restraints: 8763 sinusoidal: 3793 harmonic: 4970 Sorted by residual: dihedral pdb=" C13 A8W B 509 " pdb=" C17 A8W B 509 " pdb=" C20 A8W B 509 " pdb=" C21 A8W B 509 " ideal model delta sinusoidal sigma weight residual 275.10 121.52 153.58 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C16 A8W B 509 " pdb=" C17 A8W B 509 " pdb=" C20 A8W B 509 " pdb=" C21 A8W B 509 " ideal model delta sinusoidal sigma weight residual 154.76 1.46 153.30 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA SER B 339 " pdb=" C SER B 339 " pdb=" N TYR B 340 " pdb=" CA TYR B 340 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2093 0.091 - 0.182: 118 0.182 - 0.272: 1 0.272 - 0.363: 0 0.363 - 0.454: 1 Chirality restraints: 2213 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 140 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA ASN A 234 " pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CB ASN A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" C3 A8W B 509 " pdb=" C2 A8W B 509 " pdb=" C4 A8W B 509 " pdb=" O1 A8W B 509 " both_signs ideal model delta sigma weight residual False -2.53 -2.69 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 2210 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 140 " 0.249 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" CG ASN B 140 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN B 140 " -0.109 2.00e-02 2.50e+03 pdb=" ND2 ASN B 140 " -0.327 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.266 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 286 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C LEU A 286 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 286 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 287 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 286 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C LEU D 286 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU D 286 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN D 287 " 0.012 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 123 2.65 - 3.21: 11845 3.21 - 3.77: 19171 3.77 - 4.34: 27582 4.34 - 4.90: 48205 Nonbonded interactions: 106926 Sorted by model distance: nonbonded pdb=" ND2 ASN C 140 " pdb=" C1 NAG C 502 " model vdw 2.083 3.550 nonbonded pdb=" ND2 ASN D 140 " pdb=" C1 NAG D 502 " model vdw 2.182 3.550 nonbonded pdb=" ND2 ASN B 234 " pdb=" C1 NAG B 503 " model vdw 2.207 3.550 nonbonded pdb=" ND2 ASN A 140 " pdb=" C1 NAG A 501 " model vdw 2.217 3.550 nonbonded pdb=" OG1 THR C 265 " pdb=" OH TYR C 268 " model vdw 2.249 3.040 ... (remaining 106921 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 74 through 479 or resid 502)) selection = (chain 'B' and (resid 74 through 479 or resid 502)) selection = (chain 'C' and (resid 74 through 479 or resid 502)) selection = (chain 'D' and (resid 74 through 479 or resid 502)) selection = (chain 'E' and (resid 74 through 479 or resid 502)) } 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.370 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.005 0.405 14574 Z= 0.239 Angle : 0.652 16.176 19686 Z= 0.312 Chirality : 0.041 0.454 2213 Planarity : 0.003 0.033 2381 Dihedral : 9.290 153.578 5518 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.21), residues: 1645 helix: 1.60 (0.23), residues: 565 sheet: 1.40 (0.24), residues: 405 loop : 0.51 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 125 TYR 0.015 0.001 TYR C 340 PHE 0.010 0.001 PHE D 290 TRP 0.008 0.001 TRP B 349 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00325 (14568) covalent geometry : angle 0.63727 (19673) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.56999 ( 10) hydrogen bonds : bond 0.25012 ( 667) hydrogen bonds : angle 6.93230 ( 2049) link_NAG-ASN : bond 0.40508 ( 1) link_NAG-ASN : angle 11.09891 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8852 (mmtp) REVERT: B 181 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8079 (mm-40) REVERT: C 88 MET cc_start: 0.7213 (ptp) cc_final: 0.6706 (ptm) REVERT: C 97 ILE cc_start: 0.8637 (pt) cc_final: 0.8427 (tp) REVERT: C 120 MET cc_start: 0.8625 (ttm) cc_final: 0.8375 (ttm) REVERT: C 143 MET cc_start: 0.8399 (mtm) cc_final: 0.8124 (mtp) REVERT: C 149 LEU cc_start: 0.8855 (tp) cc_final: 0.8643 (tp) REVERT: C 170 ASP cc_start: 0.8525 (p0) cc_final: 0.8258 (p0) REVERT: C 179 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7041 (ttm-80) REVERT: C 278 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6690 (mtm-85) REVERT: C 304 TRP cc_start: 0.8519 (m100) cc_final: 0.8163 (m-90) REVERT: D 146 ASP cc_start: 0.8784 (p0) cc_final: 0.8568 (p0) REVERT: D 149 LEU cc_start: 0.9057 (tp) cc_final: 0.8833 (tt) REVERT: E 76 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7401 (mp0) REVERT: E 83 ASP cc_start: 0.7744 (m-30) cc_final: 0.7365 (t0) REVERT: E 84 HIS cc_start: 0.7230 (m90) cc_final: 0.6539 (m90) REVERT: E 117 ASP cc_start: 0.8780 (p0) cc_final: 0.8574 (p0) REVERT: E 179 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6822 (ttm170) REVERT: E 308 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7844 (mtp85) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.1492 time to fit residues: 63.2888 Evaluate side-chains 214 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 269 ASN D 199 ASN D 332 ASN E 287 GLN E 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096338 restraints weight = 18795.691| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.92 r_work: 0.2943 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14574 Z= 0.135 Angle : 0.525 5.981 19686 Z= 0.285 Chirality : 0.041 0.196 2213 Planarity : 0.004 0.054 2381 Dihedral : 6.714 137.297 2308 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.20 % Allowed : 6.21 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.21), residues: 1645 helix: 2.54 (0.23), residues: 535 sheet: 1.39 (0.25), residues: 405 loop : 0.51 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 278 TYR 0.018 0.002 TYR D 272 PHE 0.017 0.001 PHE A 356 TRP 0.012 0.001 TRP D 349 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00259 (14568) covalent geometry : angle 0.52317 (19673) SS BOND : bond 0.01083 ( 5) SS BOND : angle 0.89358 ( 10) hydrogen bonds : bond 0.07120 ( 667) hydrogen bonds : angle 4.68146 ( 2049) link_NAG-ASN : bond 0.00710 ( 1) link_NAG-ASN : angle 3.65215 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8900 (mmtp) REVERT: A 181 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7537 (mt0) REVERT: A 227 MET cc_start: 0.7495 (ttt) cc_final: 0.7221 (ttm) REVERT: A 372 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7634 (tp40) REVERT: B 76 GLU cc_start: 0.6853 (mp0) cc_final: 0.6598 (mp0) REVERT: B 181 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7859 (mt0) REVERT: B 223 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7567 (tm-30) REVERT: B 225 ASP cc_start: 0.8265 (m-30) cc_final: 0.7948 (m-30) REVERT: C 88 MET cc_start: 0.7434 (ptp) cc_final: 0.6936 (ptm) REVERT: C 170 ASP cc_start: 0.8739 (p0) cc_final: 0.8484 (p0) REVERT: C 179 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7110 (ttm170) REVERT: C 234 ASN cc_start: 0.8326 (m-40) cc_final: 0.8098 (m-40) REVERT: C 304 TRP cc_start: 0.8552 (m100) cc_final: 0.8206 (m-90) REVERT: C 373 GLU cc_start: 0.6668 (mm-30) cc_final: 0.5670 (mt-10) REVERT: D 84 HIS cc_start: 0.7595 (m90) cc_final: 0.7253 (m90) REVERT: D 111 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8203 (mt) REVERT: D 149 LEU cc_start: 0.8907 (tp) cc_final: 0.8678 (tt) REVERT: E 76 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7417 (mp0) REVERT: E 83 ASP cc_start: 0.8089 (m-30) cc_final: 0.7516 (t70) REVERT: E 84 HIS cc_start: 0.7191 (m90) cc_final: 0.6409 (m90) REVERT: E 117 ASP cc_start: 0.8964 (p0) cc_final: 0.8749 (p0) REVERT: E 179 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.7074 (ttm-80) REVERT: E 181 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.6801 (mp10) REVERT: E 308 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7868 (mtp85) outliers start: 34 outliers final: 22 residues processed: 240 average time/residue: 0.1370 time to fit residues: 46.8485 Evaluate side-chains 230 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 370 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 0.0060 chunk 78 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093876 restraints weight = 18895.185| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.93 r_work: 0.2867 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14574 Z= 0.140 Angle : 0.503 4.974 19686 Z= 0.276 Chirality : 0.041 0.150 2213 Planarity : 0.004 0.056 2381 Dihedral : 6.398 130.080 2308 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.52 % Allowed : 7.70 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.21), residues: 1645 helix: 2.57 (0.22), residues: 535 sheet: 1.19 (0.25), residues: 405 loop : 0.42 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 278 TYR 0.016 0.002 TYR D 272 PHE 0.017 0.001 PHE A 356 TRP 0.010 0.001 TRP D 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00303 (14568) covalent geometry : angle 0.50150 (19673) SS BOND : bond 0.00664 ( 5) SS BOND : angle 1.20480 ( 10) hydrogen bonds : bond 0.06740 ( 667) hydrogen bonds : angle 4.34030 ( 2049) link_NAG-ASN : bond 0.00649 ( 1) link_NAG-ASN : angle 2.80220 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8906 (mmtp) REVERT: A 181 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7534 (mt0) REVERT: B 76 GLU cc_start: 0.6929 (mp0) cc_final: 0.6676 (mp0) REVERT: B 181 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7799 (mt0) REVERT: C 88 MET cc_start: 0.7477 (ptp) cc_final: 0.6993 (ptm) REVERT: C 170 ASP cc_start: 0.8757 (p0) cc_final: 0.8515 (p0) REVERT: C 179 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7115 (ttm170) REVERT: D 84 HIS cc_start: 0.7664 (m90) cc_final: 0.7368 (m90) REVERT: D 149 LEU cc_start: 0.8942 (tp) cc_final: 0.8706 (tt) REVERT: E 76 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7454 (mp0) REVERT: E 83 ASP cc_start: 0.8111 (m-30) cc_final: 0.7568 (t70) REVERT: E 84 HIS cc_start: 0.7175 (m90) cc_final: 0.6380 (m90) REVERT: E 117 ASP cc_start: 0.8995 (p0) cc_final: 0.8773 (p0) REVERT: E 143 MET cc_start: 0.7228 (mtm) cc_final: 0.7024 (mtp) REVERT: E 179 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7028 (ttm-80) REVERT: E 181 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: E 308 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7910 (mtp85) outliers start: 39 outliers final: 28 residues processed: 239 average time/residue: 0.1368 time to fit residues: 46.7581 Evaluate side-chains 224 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN C 234 ASN C 287 GLN C 332 ASN D 287 GLN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095249 restraints weight = 18876.879| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.92 r_work: 0.2890 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14574 Z= 0.121 Angle : 0.479 6.633 19686 Z= 0.261 Chirality : 0.040 0.147 2213 Planarity : 0.004 0.059 2381 Dihedral : 6.233 127.689 2308 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.59 % Allowed : 8.67 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.21), residues: 1645 helix: 2.57 (0.22), residues: 535 sheet: 1.13 (0.25), residues: 405 loop : 0.42 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 278 TYR 0.015 0.001 TYR D 272 PHE 0.014 0.001 PHE A 356 TRP 0.009 0.001 TRP D 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00254 (14568) covalent geometry : angle 0.47773 (19673) SS BOND : bond 0.00491 ( 5) SS BOND : angle 0.98253 ( 10) hydrogen bonds : bond 0.05839 ( 667) hydrogen bonds : angle 4.09963 ( 2049) link_NAG-ASN : bond 0.00499 ( 1) link_NAG-ASN : angle 2.12103 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8905 (mmtp) REVERT: A 181 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7515 (mt0) REVERT: B 181 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7815 (mt0) REVERT: B 223 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8163 (tp30) REVERT: C 76 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: C 88 MET cc_start: 0.7502 (ptp) cc_final: 0.7002 (ptm) REVERT: C 143 MET cc_start: 0.7915 (mtm) cc_final: 0.7656 (mtt) REVERT: C 170 ASP cc_start: 0.8722 (p0) cc_final: 0.8454 (p0) REVERT: C 179 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7102 (ttm170) REVERT: C 223 GLU cc_start: 0.7880 (pt0) cc_final: 0.7466 (pm20) REVERT: C 308 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7767 (ttm110) REVERT: C 373 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5538 (mt-10) REVERT: D 84 HIS cc_start: 0.7682 (m90) cc_final: 0.7428 (m90) REVERT: D 149 LEU cc_start: 0.8923 (tp) cc_final: 0.8687 (tt) REVERT: E 76 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7455 (mp0) REVERT: E 83 ASP cc_start: 0.8130 (m-30) cc_final: 0.7610 (t70) REVERT: E 84 HIS cc_start: 0.7189 (m90) cc_final: 0.6388 (m90) REVERT: E 117 ASP cc_start: 0.8948 (p0) cc_final: 0.8711 (p0) REVERT: E 179 ARG cc_start: 0.7506 (ttp-170) cc_final: 0.6979 (ttm-80) REVERT: E 181 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: E 308 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7921 (mtp85) outliers start: 40 outliers final: 32 residues processed: 218 average time/residue: 0.1410 time to fit residues: 43.7586 Evaluate side-chains 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 123 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN C 287 GLN C 332 ASN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096686 restraints weight = 18792.732| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.92 r_work: 0.2923 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14574 Z= 0.112 Angle : 0.459 5.008 19686 Z= 0.251 Chirality : 0.039 0.144 2213 Planarity : 0.004 0.049 2381 Dihedral : 6.095 125.788 2308 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.59 % Allowed : 9.13 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.21), residues: 1645 helix: 2.57 (0.22), residues: 535 sheet: 1.15 (0.26), residues: 405 loop : 0.42 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 278 TYR 0.014 0.001 TYR D 340 PHE 0.012 0.001 PHE A 356 TRP 0.008 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00225 (14568) covalent geometry : angle 0.45852 (19673) SS BOND : bond 0.00400 ( 5) SS BOND : angle 0.90472 ( 10) hydrogen bonds : bond 0.05433 ( 667) hydrogen bonds : angle 3.96335 ( 2049) link_NAG-ASN : bond 0.00553 ( 1) link_NAG-ASN : angle 1.78094 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8898 (mmtm) REVERT: A 181 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7506 (mt0) REVERT: B 181 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7770 (mt0) REVERT: B 223 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8180 (tp30) REVERT: C 76 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: C 88 MET cc_start: 0.7525 (ptp) cc_final: 0.7020 (ptm) REVERT: C 143 MET cc_start: 0.7847 (mtm) cc_final: 0.7634 (mtt) REVERT: C 179 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7053 (ttm-80) REVERT: C 223 GLU cc_start: 0.7935 (pt0) cc_final: 0.7571 (pm20) REVERT: C 308 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7784 (ttm110) REVERT: D 84 HIS cc_start: 0.7677 (m90) cc_final: 0.7464 (m90) REVERT: D 111 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8180 (mt) REVERT: D 149 LEU cc_start: 0.8900 (tp) cc_final: 0.8662 (tt) REVERT: E 76 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7470 (mp0) REVERT: E 83 ASP cc_start: 0.8135 (m-30) cc_final: 0.7643 (t70) REVERT: E 84 HIS cc_start: 0.7176 (m90) cc_final: 0.6356 (m90) REVERT: E 92 PHE cc_start: 0.8667 (t80) cc_final: 0.8400 (t80) REVERT: E 117 ASP cc_start: 0.8891 (p0) cc_final: 0.8643 (p0) REVERT: E 143 MET cc_start: 0.6932 (mtp) cc_final: 0.6507 (mtm) REVERT: E 179 ARG cc_start: 0.7472 (ttp-170) cc_final: 0.6973 (ttm-80) REVERT: E 181 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6526 (mp10) REVERT: E 308 ARG cc_start: 0.8207 (mtm180) cc_final: 0.7822 (mtp85) outliers start: 40 outliers final: 28 residues processed: 215 average time/residue: 0.1381 time to fit residues: 42.8050 Evaluate side-chains 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.091928 restraints weight = 18912.240| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.91 r_work: 0.2823 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14574 Z= 0.179 Angle : 0.545 6.620 19686 Z= 0.297 Chirality : 0.042 0.158 2213 Planarity : 0.004 0.047 2381 Dihedral : 6.484 126.608 2308 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.85 % Allowed : 9.39 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.21), residues: 1645 helix: 2.42 (0.22), residues: 535 sheet: 1.00 (0.25), residues: 405 loop : 0.25 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.016 0.002 TYR A 362 PHE 0.017 0.002 PHE C 356 TRP 0.009 0.001 TRP D 349 HIS 0.006 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00427 (14568) covalent geometry : angle 0.54345 (19673) SS BOND : bond 0.00598 ( 5) SS BOND : angle 1.41676 ( 10) hydrogen bonds : bond 0.06828 ( 667) hydrogen bonds : angle 4.18245 ( 2049) link_NAG-ASN : bond 0.00578 ( 1) link_NAG-ASN : angle 1.74415 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8908 (mmtp) REVERT: A 157 ASP cc_start: 0.8811 (p0) cc_final: 0.8605 (p0) REVERT: A 181 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7512 (mt0) REVERT: B 181 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7784 (mt0) REVERT: B 223 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 76 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 88 MET cc_start: 0.7563 (ptp) cc_final: 0.7068 (ptm) REVERT: C 143 MET cc_start: 0.7851 (mtm) cc_final: 0.7583 (mtt) REVERT: C 179 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7065 (ttm-80) REVERT: C 223 GLU cc_start: 0.8155 (pt0) cc_final: 0.7845 (pm20) REVERT: C 308 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7843 (ttm110) REVERT: D 111 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8320 (mt) REVERT: D 149 LEU cc_start: 0.8956 (tp) cc_final: 0.8710 (tt) REVERT: D 242 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7461 (mtp85) REVERT: E 76 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7522 (mp0) REVERT: E 83 ASP cc_start: 0.8131 (m-30) cc_final: 0.7654 (t70) REVERT: E 84 HIS cc_start: 0.7176 (m90) cc_final: 0.6372 (m90) REVERT: E 92 PHE cc_start: 0.8666 (t80) cc_final: 0.8426 (t80) REVERT: E 117 ASP cc_start: 0.9011 (p0) cc_final: 0.8786 (p0) REVERT: E 179 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.6985 (ttm-80) REVERT: E 181 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6582 (mp10) REVERT: E 308 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7828 (mtp85) outliers start: 44 outliers final: 36 residues processed: 223 average time/residue: 0.1451 time to fit residues: 46.0359 Evaluate side-chains 227 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 287 GLN C 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098670 restraints weight = 19054.766| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.48 r_work: 0.2926 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14574 Z= 0.114 Angle : 0.470 6.521 19686 Z= 0.256 Chirality : 0.040 0.145 2213 Planarity : 0.004 0.042 2381 Dihedral : 6.274 124.864 2308 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.27 % Allowed : 10.81 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.21), residues: 1645 helix: 2.51 (0.22), residues: 535 sheet: 1.07 (0.26), residues: 405 loop : 0.32 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.015 0.001 TYR D 340 PHE 0.011 0.001 PHE A 356 TRP 0.009 0.001 TRP B 349 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00234 (14568) covalent geometry : angle 0.46918 (19673) SS BOND : bond 0.00398 ( 5) SS BOND : angle 0.87351 ( 10) hydrogen bonds : bond 0.05484 ( 667) hydrogen bonds : angle 3.96522 ( 2049) link_NAG-ASN : bond 0.00543 ( 1) link_NAG-ASN : angle 1.42641 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8962 (mmtp) REVERT: A 157 ASP cc_start: 0.8770 (p0) cc_final: 0.8556 (p0) REVERT: A 181 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7589 (mt0) REVERT: B 181 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7904 (mt0) REVERT: B 223 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8376 (tp30) REVERT: C 76 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: C 88 MET cc_start: 0.7697 (ptp) cc_final: 0.7199 (ptm) REVERT: C 143 MET cc_start: 0.7942 (mtm) cc_final: 0.7721 (mtt) REVERT: C 179 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7300 (ttm-80) REVERT: C 223 GLU cc_start: 0.8129 (pt0) cc_final: 0.7759 (pm20) REVERT: C 308 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7814 (ttm110) REVERT: D 111 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 149 LEU cc_start: 0.9035 (tp) cc_final: 0.8805 (tt) REVERT: E 76 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7607 (mp0) REVERT: E 83 ASP cc_start: 0.8167 (m-30) cc_final: 0.7701 (t70) REVERT: E 84 HIS cc_start: 0.7186 (m90) cc_final: 0.6377 (m90) REVERT: E 117 ASP cc_start: 0.8986 (p0) cc_final: 0.8776 (p0) REVERT: E 143 MET cc_start: 0.7089 (mtp) cc_final: 0.6746 (mtm) REVERT: E 179 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7222 (ttm-80) REVERT: E 181 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: E 308 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7774 (mtp85) outliers start: 35 outliers final: 28 residues processed: 205 average time/residue: 0.1347 time to fit residues: 39.9455 Evaluate side-chains 211 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 158 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN C 332 ASN E 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099135 restraints weight = 18981.562| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.52 r_work: 0.2954 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14574 Z= 0.103 Angle : 0.452 6.489 19686 Z= 0.246 Chirality : 0.039 0.142 2213 Planarity : 0.004 0.071 2381 Dihedral : 5.984 123.017 2308 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 11.46 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.21), residues: 1645 helix: 2.56 (0.22), residues: 535 sheet: 1.17 (0.26), residues: 405 loop : 0.39 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.015 0.001 TYR D 340 PHE 0.009 0.001 PHE A 356 TRP 0.008 0.001 TRP B 349 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00198 (14568) covalent geometry : angle 0.45198 (19673) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.75929 ( 10) hydrogen bonds : bond 0.04825 ( 667) hydrogen bonds : angle 3.81707 ( 2049) link_NAG-ASN : bond 0.00559 ( 1) link_NAG-ASN : angle 1.22716 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8958 (mmtp) REVERT: A 157 ASP cc_start: 0.8815 (p0) cc_final: 0.8590 (p0) REVERT: A 181 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7540 (mt0) REVERT: B 181 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8030 (mt0) REVERT: B 223 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8358 (tp30) REVERT: C 76 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: C 88 MET cc_start: 0.7687 (ptp) cc_final: 0.7181 (ptm) REVERT: C 143 MET cc_start: 0.7880 (mtm) cc_final: 0.7669 (mtt) REVERT: C 179 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7287 (ttm-80) REVERT: C 223 GLU cc_start: 0.8052 (pt0) cc_final: 0.7718 (pm20) REVERT: C 308 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7773 (ttm110) REVERT: D 111 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8188 (mt) REVERT: D 149 LEU cc_start: 0.8989 (tp) cc_final: 0.8760 (tt) REVERT: E 76 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7621 (mp0) REVERT: E 83 ASP cc_start: 0.8171 (m-30) cc_final: 0.7706 (t70) REVERT: E 84 HIS cc_start: 0.7217 (m90) cc_final: 0.6378 (m90) REVERT: E 117 ASP cc_start: 0.8938 (p0) cc_final: 0.8714 (p0) REVERT: E 179 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7185 (ttm110) REVERT: E 308 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7785 (mtp85) outliers start: 32 outliers final: 23 residues processed: 206 average time/residue: 0.1240 time to fit residues: 37.1361 Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100613 restraints weight = 19005.522| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.42 r_work: 0.2958 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14574 Z= 0.105 Angle : 0.455 6.307 19686 Z= 0.248 Chirality : 0.039 0.144 2213 Planarity : 0.004 0.072 2381 Dihedral : 5.931 122.748 2308 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.07 % Allowed : 11.46 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.21), residues: 1645 helix: 2.63 (0.22), residues: 535 sheet: 1.20 (0.26), residues: 405 loop : 0.38 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.015 0.001 TYR D 340 PHE 0.032 0.001 PHE E 92 TRP 0.008 0.001 TRP B 349 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00215 (14568) covalent geometry : angle 0.45500 (19673) SS BOND : bond 0.00351 ( 5) SS BOND : angle 0.81676 ( 10) hydrogen bonds : bond 0.04819 ( 667) hydrogen bonds : angle 3.77388 ( 2049) link_NAG-ASN : bond 0.00545 ( 1) link_NAG-ASN : angle 1.21374 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.440 Fit side-chains REVERT: A 151 LYS cc_start: 0.9247 (mmtt) cc_final: 0.8933 (mmtp) REVERT: A 157 ASP cc_start: 0.8800 (p0) cc_final: 0.8591 (p0) REVERT: A 181 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7548 (mt0) REVERT: B 181 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8027 (mt0) REVERT: B 223 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8347 (tp30) REVERT: C 76 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: C 143 MET cc_start: 0.7873 (mtm) cc_final: 0.7670 (mtt) REVERT: C 179 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7316 (ttm-80) REVERT: C 223 GLU cc_start: 0.8055 (pt0) cc_final: 0.7735 (pm20) REVERT: C 308 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7758 (ttm110) REVERT: D 111 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 149 LEU cc_start: 0.8990 (tp) cc_final: 0.8763 (tt) REVERT: E 76 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7611 (mp0) REVERT: E 83 ASP cc_start: 0.8165 (m-30) cc_final: 0.7703 (t70) REVERT: E 84 HIS cc_start: 0.7213 (m90) cc_final: 0.6371 (m90) REVERT: E 117 ASP cc_start: 0.8928 (p0) cc_final: 0.8686 (p0) REVERT: E 143 MET cc_start: 0.6964 (mtp) cc_final: 0.6698 (mtm) REVERT: E 179 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7175 (ttm-80) REVERT: E 308 ARG cc_start: 0.8247 (mtm180) cc_final: 0.7790 (mtp85) outliers start: 32 outliers final: 28 residues processed: 204 average time/residue: 0.1236 time to fit residues: 36.5408 Evaluate side-chains 210 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098357 restraints weight = 19081.220| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.41 r_work: 0.2907 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14574 Z= 0.144 Angle : 0.506 5.963 19686 Z= 0.277 Chirality : 0.041 0.153 2213 Planarity : 0.004 0.067 2381 Dihedral : 6.131 123.175 2308 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.07 % Allowed : 11.97 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.21), residues: 1645 helix: 2.62 (0.22), residues: 525 sheet: 1.13 (0.26), residues: 405 loop : 0.28 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.014 0.002 TYR C 340 PHE 0.014 0.001 PHE C 356 TRP 0.008 0.001 TRP B 349 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00329 (14568) covalent geometry : angle 0.50566 (19673) SS BOND : bond 0.00487 ( 5) SS BOND : angle 1.12083 ( 10) hydrogen bonds : bond 0.05769 ( 667) hydrogen bonds : angle 3.90307 ( 2049) link_NAG-ASN : bond 0.00556 ( 1) link_NAG-ASN : angle 1.31468 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7974 (ttp) cc_final: 0.7646 (ttp) REVERT: A 151 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8934 (mmtp) REVERT: A 181 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7568 (mt0) REVERT: B 181 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7947 (mt0) REVERT: C 76 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: C 143 MET cc_start: 0.7898 (mtm) cc_final: 0.7672 (mtt) REVERT: C 179 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7336 (ttm-80) REVERT: C 223 GLU cc_start: 0.8161 (pt0) cc_final: 0.7932 (pm20) REVERT: C 308 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7803 (ttm110) REVERT: D 111 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8341 (mt) REVERT: D 149 LEU cc_start: 0.9026 (tp) cc_final: 0.8791 (tt) REVERT: D 242 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7558 (mtp85) REVERT: E 76 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7627 (mp0) REVERT: E 83 ASP cc_start: 0.8157 (m-30) cc_final: 0.7728 (t70) REVERT: E 84 HIS cc_start: 0.7198 (m90) cc_final: 0.6352 (m90) REVERT: E 117 ASP cc_start: 0.8995 (p0) cc_final: 0.8791 (p0) REVERT: E 143 MET cc_start: 0.6951 (mtp) cc_final: 0.6687 (mtm) REVERT: E 179 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7194 (ttm-80) REVERT: E 308 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7780 (mtp85) outliers start: 32 outliers final: 28 residues processed: 204 average time/residue: 0.1317 time to fit residues: 38.8663 Evaluate side-chains 212 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN D 274 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.095790 restraints weight = 19173.967| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.50 r_work: 0.2866 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14574 Z= 0.156 Angle : 0.517 6.356 19686 Z= 0.283 Chirality : 0.041 0.154 2213 Planarity : 0.004 0.066 2381 Dihedral : 6.288 123.586 2308 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.07 % Allowed : 12.10 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.21), residues: 1645 helix: 2.53 (0.22), residues: 525 sheet: 1.07 (0.26), residues: 405 loop : 0.19 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.014 0.002 TYR A 362 PHE 0.035 0.002 PHE B 92 TRP 0.007 0.001 TRP A 349 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00364 (14568) covalent geometry : angle 0.51589 (19673) SS BOND : bond 0.00512 ( 5) SS BOND : angle 1.16352 ( 10) hydrogen bonds : bond 0.06101 ( 667) hydrogen bonds : angle 3.98317 ( 2049) link_NAG-ASN : bond 0.00558 ( 1) link_NAG-ASN : angle 1.37206 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.55 seconds wall clock time: 60 minutes 22.80 seconds (3622.80 seconds total)