Starting phenix.real_space_refine on Thu Jun 12 18:42:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh9_19173/06_2025/8rh9_19173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh9_19173/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rh9_19173/06_2025/8rh9_19173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh9_19173/06_2025/8rh9_19173.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh9_19173/06_2025/8rh9_19173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh9_19173/06_2025/8rh9_19173.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.36, per 1000 atoms: 0.73 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: 3.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.53 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: 4.41 Time building geometry restraints manager: 4.13 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: 45.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.990 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (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 TRP 0.008 0.001 TRP B 349 HIS 0.003 0.001 HIS D 254 PHE 0.010 0.001 PHE D 290 TYR 0.015 0.001 TYR C 340 ARG 0.001 0.000 ARG B 125 Details of bonding type rmsd link_NAG-ASN : bond 0.40508 ( 1) link_NAG-ASN : angle 11.09891 ( 3) hydrogen bonds : bond 0.25012 ( 667) hydrogen bonds : angle 6.93230 ( 2049) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.56999 ( 10) covalent geometry : bond 0.00325 (14568) covalent geometry : angle 0.63727 (19673) *********************** 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 : 1.589 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: 0.2961 time to fit residues: 125.6201 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 : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3517 r_free = 0.3517 target = 0.129179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.094558 restraints weight = 18706.086| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.92 r_work: 0.2916 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14574 Z= 0.151 Angle : 0.545 6.023 19686 Z= 0.297 Chirality : 0.042 0.209 2213 Planarity : 0.004 0.055 2381 Dihedral : 6.845 138.012 2308 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.52 % Allowed : 6.15 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1645 helix: 2.08 (0.22), residues: 570 sheet: 1.26 (0.25), residues: 405 loop : 0.38 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 349 HIS 0.005 0.001 HIS D 254 PHE 0.018 0.001 PHE A 356 TYR 0.019 0.002 TYR D 272 ARG 0.003 0.000 ARG E 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 3.56042 ( 3) hydrogen bonds : bond 0.07377 ( 667) hydrogen bonds : angle 4.69453 ( 2049) SS BOND : bond 0.00722 ( 5) SS BOND : angle 1.11191 ( 10) covalent geometry : bond 0.00320 (14568) covalent geometry : angle 0.54303 (19673) *********************** 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 264 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8903 (mmtp) REVERT: A 181 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7551 (mt0) REVERT: A 227 MET cc_start: 0.7559 (ttt) cc_final: 0.7217 (ttm) REVERT: A 372 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7641 (tp40) REVERT: B 76 GLU cc_start: 0.6902 (mp0) cc_final: 0.6582 (mp0) REVERT: B 181 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7858 (mt0) REVERT: B 223 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 225 ASP cc_start: 0.8277 (m-30) cc_final: 0.8001 (m-30) REVERT: C 88 MET cc_start: 0.7461 (ptp) cc_final: 0.6970 (ptm) REVERT: C 170 ASP cc_start: 0.8754 (p0) cc_final: 0.8484 (p0) REVERT: C 179 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7117 (ttm-80) REVERT: C 234 ASN cc_start: 0.8387 (m-40) cc_final: 0.8162 (m-40) REVERT: C 278 ARG cc_start: 0.7733 (mtt-85) cc_final: 0.7529 (mtp85) REVERT: C 304 TRP cc_start: 0.8569 (m100) cc_final: 0.8190 (m-90) REVERT: C 373 GLU cc_start: 0.6742 (mm-30) cc_final: 0.5609 (mt-10) REVERT: D 84 HIS cc_start: 0.7614 (m90) cc_final: 0.7278 (m90) REVERT: D 111 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8234 (mt) REVERT: D 149 LEU cc_start: 0.8963 (tp) cc_final: 0.8730 (tt) REVERT: E 83 ASP cc_start: 0.8094 (m-30) cc_final: 0.7524 (t70) REVERT: E 84 HIS cc_start: 0.7192 (m90) cc_final: 0.6434 (m90) REVERT: E 117 ASP cc_start: 0.8993 (p0) cc_final: 0.8793 (p0) REVERT: E 179 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7079 (ttm-80) REVERT: E 181 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.6838 (mp10) REVERT: E 308 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7889 (mtp85) outliers start: 39 outliers final: 28 residues processed: 246 average time/residue: 0.3389 time to fit residues: 118.2888 Evaluate side-chains 244 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 2.064 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain A residue 370 THR 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 B residue 452 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 457 LYS 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 457 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 162 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 139 ASN D 199 ASN D 274 ASN E 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.090453 restraints weight = 18970.046| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.89 r_work: 0.2794 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14574 Z= 0.214 Angle : 0.591 6.545 19686 Z= 0.324 Chirality : 0.044 0.161 2213 Planarity : 0.005 0.060 2381 Dihedral : 7.030 131.845 2308 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.17 % Allowed : 7.70 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1645 helix: 1.89 (0.22), residues: 570 sheet: 0.83 (0.23), residues: 445 loop : 0.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 349 HIS 0.006 0.002 HIS D 254 PHE 0.022 0.002 PHE C 356 TYR 0.019 0.002 TYR D 272 ARG 0.007 0.000 ARG E 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 1) link_NAG-ASN : angle 2.94154 ( 3) hydrogen bonds : bond 0.08075 ( 667) hydrogen bonds : angle 4.59048 ( 2049) SS BOND : bond 0.00813 ( 5) SS BOND : angle 1.78873 ( 10) covalent geometry : bond 0.00513 (14568) covalent geometry : angle 0.58896 (19673) *********************** 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 256 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8913 (mmtp) REVERT: A 181 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7570 (mt0) REVERT: B 76 GLU cc_start: 0.7008 (mp0) cc_final: 0.6736 (mp0) REVERT: B 223 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7899 (tm-30) REVERT: C 76 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7511 (pm20) REVERT: C 88 MET cc_start: 0.7556 (ptp) cc_final: 0.7067 (ptm) REVERT: C 170 ASP cc_start: 0.8753 (p0) cc_final: 0.8528 (p0) REVERT: C 179 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7140 (ttm-80) REVERT: D 84 HIS cc_start: 0.7676 (m90) cc_final: 0.7375 (m90) REVERT: D 149 LEU cc_start: 0.9050 (tp) cc_final: 0.8817 (tt) REVERT: D 242 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7401 (mtp85) REVERT: E 83 ASP cc_start: 0.8095 (m-30) cc_final: 0.7575 (t70) REVERT: E 84 HIS cc_start: 0.7209 (m90) cc_final: 0.6445 (m90) REVERT: E 117 ASP cc_start: 0.9067 (p0) cc_final: 0.8843 (p0) REVERT: E 179 ARG cc_start: 0.7642 (ttp-170) cc_final: 0.7210 (ttm170) REVERT: E 181 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: E 308 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7889 (mtp85) outliers start: 49 outliers final: 36 residues processed: 236 average time/residue: 0.3185 time to fit residues: 108.2407 Evaluate side-chains 226 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 468 ILE 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 197 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 457 LYS 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 16 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN C 234 ASN D 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.093578 restraints weight = 18727.979| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.91 r_work: 0.2903 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2372 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= 0.131 Angle : 0.501 5.074 19686 Z= 0.275 Chirality : 0.040 0.151 2213 Planarity : 0.004 0.047 2381 Dihedral : 6.704 128.559 2308 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.52 % Allowed : 9.13 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1645 helix: 2.39 (0.22), residues: 535 sheet: 0.93 (0.25), residues: 405 loop : 0.26 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS A 254 PHE 0.015 0.001 PHE A 356 TYR 0.016 0.002 TYR D 340 ARG 0.003 0.000 ARG E 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 1) link_NAG-ASN : angle 2.22891 ( 3) hydrogen bonds : bond 0.06391 ( 667) hydrogen bonds : angle 4.27393 ( 2049) SS BOND : bond 0.00480 ( 5) SS BOND : angle 1.05715 ( 10) covalent geometry : bond 0.00278 (14568) covalent geometry : angle 0.50000 (19673) *********************** 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 241 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8906 (mmtp) REVERT: A 181 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7531 (mt0) REVERT: B 181 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8006 (mt0) REVERT: B 223 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 76 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7547 (pm20) REVERT: C 88 MET cc_start: 0.7548 (ptp) cc_final: 0.7055 (ptm) REVERT: C 170 ASP cc_start: 0.8720 (p0) cc_final: 0.8467 (p0) REVERT: C 179 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7111 (ttm-80) REVERT: D 84 HIS cc_start: 0.7680 (m90) cc_final: 0.7398 (m90) REVERT: D 149 LEU cc_start: 0.8998 (tp) cc_final: 0.8779 (tt) REVERT: D 242 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7434 (mtp85) REVERT: E 83 ASP cc_start: 0.8119 (m-30) cc_final: 0.7622 (t70) REVERT: E 84 HIS cc_start: 0.7231 (m90) cc_final: 0.6446 (m90) REVERT: E 179 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.6998 (ttm-80) REVERT: E 181 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6662 (mp10) REVERT: E 308 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7868 (mtp85) outliers start: 39 outliers final: 30 residues processed: 224 average time/residue: 0.3181 time to fit residues: 103.5133 Evaluate side-chains 224 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 256 THR 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 369 THR Chi-restraints excluded: chain B residue 371 VAL 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 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 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 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 97 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 372 GLN D 199 ASN ** E 332 ASN ** 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 = 0.3498 r_free = 0.3498 target = 0.127851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093337 restraints weight = 18772.902| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.91 r_work: 0.2868 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2490 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= 0.139 Angle : 0.503 5.807 19686 Z= 0.275 Chirality : 0.041 0.151 2213 Planarity : 0.004 0.063 2381 Dihedral : 6.551 126.541 2308 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.72 % Allowed : 10.03 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1645 helix: 2.41 (0.22), residues: 535 sheet: 0.91 (0.25), residues: 405 loop : 0.24 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.005 0.001 HIS D 254 PHE 0.015 0.001 PHE A 356 TYR 0.016 0.002 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 1) link_NAG-ASN : angle 1.87998 ( 3) hydrogen bonds : bond 0.06240 ( 667) hydrogen bonds : angle 4.15998 ( 2049) SS BOND : bond 0.00490 ( 5) SS BOND : angle 1.12448 ( 10) covalent geometry : bond 0.00311 (14568) covalent geometry : angle 0.50158 (19673) *********************** 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 237 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 3.198 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8907 (mmtp) REVERT: A 181 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7511 (mt0) REVERT: B 76 GLU cc_start: 0.6902 (mp0) cc_final: 0.6677 (mp0) REVERT: B 181 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7990 (mt0) REVERT: B 223 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8359 (tp30) REVERT: C 76 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7564 (pm20) REVERT: C 88 MET cc_start: 0.7600 (ptp) cc_final: 0.7093 (ptm) REVERT: C 143 MET cc_start: 0.7854 (mtm) cc_final: 0.7619 (mtt) REVERT: C 179 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7060 (ttm-80) REVERT: C 223 GLU cc_start: 0.8095 (pt0) cc_final: 0.7652 (pm20) REVERT: C 308 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7942 (ttm110) REVERT: D 84 HIS cc_start: 0.7706 (m90) cc_final: 0.7464 (m90) REVERT: D 111 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8293 (mt) REVERT: D 149 LEU cc_start: 0.8990 (tp) cc_final: 0.8776 (tt) REVERT: D 242 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7449 (mtp85) REVERT: E 83 ASP cc_start: 0.8126 (m-30) cc_final: 0.7650 (t70) REVERT: E 84 HIS cc_start: 0.7196 (m90) cc_final: 0.6395 (m90) REVERT: E 179 ARG cc_start: 0.7544 (ttp-170) cc_final: 0.6981 (ttm-80) REVERT: E 181 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6604 (mp10) REVERT: E 308 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7820 (mtp85) outliers start: 42 outliers final: 33 residues processed: 219 average time/residue: 0.3972 time to fit residues: 127.4110 Evaluate side-chains 216 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 256 THR 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN E 234 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 = 0.3479 r_free = 0.3479 target = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.092070 restraints weight = 19000.423| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.92 r_work: 0.2897 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14574 Z= 0.141 Angle : 0.505 5.005 19686 Z= 0.276 Chirality : 0.041 0.152 2213 Planarity : 0.004 0.054 2381 Dihedral : 6.492 125.586 2308 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.78 % Allowed : 10.36 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1645 helix: 2.40 (0.22), residues: 535 sheet: 0.91 (0.25), residues: 405 loop : 0.17 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.005 0.001 HIS D 254 PHE 0.022 0.001 PHE E 92 TYR 0.016 0.002 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 1) link_NAG-ASN : angle 1.65729 ( 3) hydrogen bonds : bond 0.06141 ( 667) hydrogen bonds : angle 4.11321 ( 2049) SS BOND : bond 0.00483 ( 5) SS BOND : angle 1.10491 ( 10) covalent geometry : bond 0.00319 (14568) covalent geometry : angle 0.50395 (19673) *********************** 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 234 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8902 (mmtp) REVERT: A 181 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7498 (mt0) REVERT: B 181 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8024 (mt0) REVERT: B 223 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8396 (tp30) REVERT: C 76 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7539 (pm20) REVERT: C 179 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7077 (ttm-80) REVERT: C 223 GLU cc_start: 0.8126 (pt0) cc_final: 0.7869 (pm20) REVERT: C 308 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7915 (ttm110) REVERT: D 84 HIS cc_start: 0.7708 (m90) cc_final: 0.7470 (m90) REVERT: D 111 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8293 (mt) REVERT: D 149 LEU cc_start: 0.8985 (tp) cc_final: 0.8767 (tt) REVERT: D 242 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7448 (mtp85) REVERT: E 83 ASP cc_start: 0.8143 (m-30) cc_final: 0.7704 (t70) REVERT: E 84 HIS cc_start: 0.7178 (m90) cc_final: 0.6381 (m90) REVERT: E 151 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8564 (mmtm) REVERT: E 179 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.6984 (ttm-80) REVERT: E 181 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: E 308 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7817 (mtp85) outliers start: 43 outliers final: 33 residues processed: 215 average time/residue: 0.2865 time to fit residues: 89.2423 Evaluate side-chains 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 256 THR 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 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 332 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 452 THR 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 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 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 124 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 332 ASN D 287 GLN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097284 restraints weight = 19170.550| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.44 r_work: 0.2962 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14574 Z= 0.119 Angle : 0.479 5.012 19686 Z= 0.262 Chirality : 0.040 0.147 2213 Planarity : 0.004 0.069 2381 Dihedral : 6.282 124.231 2308 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.65 % Allowed : 10.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1645 helix: 2.48 (0.22), residues: 535 sheet: 0.97 (0.25), residues: 405 loop : 0.21 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.004 0.001 HIS D 254 PHE 0.032 0.001 PHE E 92 TYR 0.016 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 1) link_NAG-ASN : angle 1.46563 ( 3) hydrogen bonds : bond 0.05619 ( 667) hydrogen bonds : angle 4.01038 ( 2049) SS BOND : bond 0.00404 ( 5) SS BOND : angle 0.91701 ( 10) covalent geometry : bond 0.00251 (14568) covalent geometry : angle 0.47866 (19673) *********************** 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 233 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8946 (mmtp) REVERT: A 181 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7532 (mt0) REVERT: B 181 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8108 (mt0) REVERT: B 223 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8463 (tp30) REVERT: C 76 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7549 (pm20) REVERT: C 179 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7255 (ttm-80) REVERT: C 223 GLU cc_start: 0.8130 (pt0) cc_final: 0.7906 (pm20) REVERT: C 308 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7891 (ttm110) REVERT: D 84 HIS cc_start: 0.7763 (m90) cc_final: 0.7558 (m90) REVERT: D 111 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8313 (mt) REVERT: D 149 LEU cc_start: 0.9047 (tp) cc_final: 0.8830 (tt) REVERT: D 242 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7516 (mtp85) REVERT: E 83 ASP cc_start: 0.8167 (m-30) cc_final: 0.7708 (t70) REVERT: E 84 HIS cc_start: 0.7246 (m90) cc_final: 0.6463 (m90) REVERT: E 179 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7202 (ttm-80) REVERT: E 181 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6617 (mp10) REVERT: E 308 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7731 (mtp85) outliers start: 41 outliers final: 30 residues processed: 216 average time/residue: 0.2878 time to fit residues: 89.2490 Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 332 ASN 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 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 360 LEU 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 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 370 THR 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 35 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097659 restraints weight = 18985.463| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.42 r_work: 0.2899 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14574 Z= 0.120 Angle : 0.481 4.981 19686 Z= 0.264 Chirality : 0.040 0.147 2213 Planarity : 0.004 0.061 2381 Dihedral : 6.173 123.658 2308 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.46 % Allowed : 11.33 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1645 helix: 2.50 (0.22), residues: 535 sheet: 1.01 (0.25), residues: 405 loop : 0.22 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 349 HIS 0.004 0.001 HIS D 254 PHE 0.034 0.001 PHE E 92 TYR 0.016 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 1) link_NAG-ASN : angle 1.39512 ( 3) hydrogen bonds : bond 0.05496 ( 667) hydrogen bonds : angle 3.96812 ( 2049) SS BOND : bond 0.00402 ( 5) SS BOND : angle 0.91528 ( 10) covalent geometry : bond 0.00256 (14568) covalent geometry : angle 0.48088 (19673) *********************** 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 226 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8959 (mmtp) REVERT: A 181 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7533 (mt0) REVERT: B 181 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8120 (mt0) REVERT: B 223 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8476 (tp30) REVERT: C 76 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7543 (pm20) REVERT: C 179 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7283 (ttm-80) REVERT: C 223 GLU cc_start: 0.8122 (pt0) cc_final: 0.7920 (pm20) REVERT: C 308 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7867 (ttm110) REVERT: D 111 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8300 (mt) REVERT: D 149 LEU cc_start: 0.9044 (tp) cc_final: 0.8826 (tt) REVERT: D 242 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7526 (mtp85) REVERT: E 83 ASP cc_start: 0.8188 (m-30) cc_final: 0.7713 (t70) REVERT: E 84 HIS cc_start: 0.7266 (m90) cc_final: 0.6474 (m90) REVERT: E 179 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7236 (ttm-80) REVERT: E 181 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: E 308 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7743 (mtp85) outliers start: 38 outliers final: 32 residues processed: 211 average time/residue: 0.2859 time to fit residues: 86.5794 Evaluate side-chains 217 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 332 ASN 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 452 THR 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 360 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 471 ASN 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 457 LYS 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 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 110 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095389 restraints weight = 19100.130| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.42 r_work: 0.2905 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14574 Z= 0.162 Angle : 0.528 5.021 19686 Z= 0.289 Chirality : 0.041 0.155 2213 Planarity : 0.004 0.074 2381 Dihedral : 6.365 124.348 2308 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 11.20 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1645 helix: 2.43 (0.22), residues: 535 sheet: 0.93 (0.25), residues: 405 loop : 0.12 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 349 HIS 0.005 0.001 HIS D 254 PHE 0.034 0.002 PHE E 92 TYR 0.015 0.002 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 1) link_NAG-ASN : angle 1.50207 ( 3) hydrogen bonds : bond 0.06294 ( 667) hydrogen bonds : angle 4.08414 ( 2049) SS BOND : bond 0.00528 ( 5) SS BOND : angle 1.20650 ( 10) covalent geometry : bond 0.00380 (14568) covalent geometry : angle 0.52732 (19673) *********************** 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 231 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8936 (mmtp) REVERT: A 181 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7467 (mt0) REVERT: B 181 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8107 (mt0) REVERT: B 223 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8488 (tp30) REVERT: C 179 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7219 (ttm-80) REVERT: C 223 GLU cc_start: 0.8231 (pt0) cc_final: 0.7951 (pm20) REVERT: C 308 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7892 (ttm110) REVERT: D 111 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8341 (mt) REVERT: D 149 LEU cc_start: 0.9027 (tp) cc_final: 0.8800 (tt) REVERT: D 242 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7552 (mtp85) REVERT: E 83 ASP cc_start: 0.8147 (m-30) cc_final: 0.7726 (t70) REVERT: E 84 HIS cc_start: 0.7220 (m90) cc_final: 0.6428 (m90) REVERT: E 179 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7178 (ttm-80) REVERT: E 181 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: E 308 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7721 (mtp85) outliers start: 42 outliers final: 36 residues processed: 214 average time/residue: 0.2846 time to fit residues: 87.5815 Evaluate side-chains 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 332 ASN 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 371 VAL Chi-restraints excluded: chain B residue 452 THR 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 360 LEU 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 C residue 471 ASN 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 371 VAL Chi-restraints excluded: chain D residue 457 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 0.6980 chunk 155 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098484 restraints weight = 18979.663| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.42 r_work: 0.2939 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14574 Z= 0.124 Angle : 0.493 5.884 19686 Z= 0.269 Chirality : 0.040 0.149 2213 Planarity : 0.004 0.071 2381 Dihedral : 6.169 123.057 2308 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.20 % Allowed : 11.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1645 helix: 2.50 (0.22), residues: 535 sheet: 1.01 (0.26), residues: 405 loop : 0.16 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.034 0.001 PHE E 92 TYR 0.016 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 1) link_NAG-ASN : angle 1.37721 ( 3) hydrogen bonds : bond 0.05586 ( 667) hydrogen bonds : angle 3.97484 ( 2049) SS BOND : bond 0.00402 ( 5) SS BOND : angle 0.90796 ( 10) covalent geometry : bond 0.00268 (14568) covalent geometry : angle 0.49263 (19673) ********************** 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 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8967 (mmtp) REVERT: A 181 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7625 (mt0) REVERT: C 76 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7486 (pm20) REVERT: C 179 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7238 (ttm-80) REVERT: C 223 GLU cc_start: 0.8197 (pt0) cc_final: 0.7976 (pm20) REVERT: C 308 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7881 (ttm110) REVERT: D 111 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8289 (mt) REVERT: D 149 LEU cc_start: 0.9021 (tp) cc_final: 0.8796 (tt) REVERT: D 242 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7519 (mtp85) REVERT: E 83 ASP cc_start: 0.8175 (m-30) cc_final: 0.7740 (t70) REVERT: E 84 HIS cc_start: 0.7268 (m90) cc_final: 0.6487 (m90) REVERT: E 179 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7182 (ttm170) REVERT: E 181 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6618 (mp10) REVERT: E 308 ARG cc_start: 0.8177 (mtm180) cc_final: 0.7704 (mtp85) outliers start: 34 outliers final: 31 residues processed: 207 average time/residue: 0.2816 time to fit residues: 83.7862 Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 332 ASN 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 452 THR 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 360 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 471 ASN 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 326 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: 5.9990 chunk 11 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097983 restraints weight = 19085.825| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.41 r_work: 0.2983 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14574 Z= 0.129 Angle : 0.496 5.162 19686 Z= 0.271 Chirality : 0.040 0.148 2213 Planarity : 0.004 0.076 2381 Dihedral : 6.137 122.411 2308 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.20 % Allowed : 12.04 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.21), residues: 1645 helix: 2.51 (0.22), residues: 535 sheet: 1.01 (0.26), residues: 405 loop : 0.14 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.035 0.001 PHE E 92 TYR 0.016 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 1.38114 ( 3) hydrogen bonds : bond 0.05659 ( 667) hydrogen bonds : angle 3.96531 ( 2049) SS BOND : bond 0.00424 ( 5) SS BOND : angle 0.97430 ( 10) covalent geometry : bond 0.00289 (14568) covalent geometry : angle 0.49532 (19673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7559.00 seconds wall clock time: 135 minutes 15.86 seconds (8115.86 seconds total)