Starting phenix.real_space_refine on Thu Sep 26 21:59:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh9_19173/09_2024/8rh9_19173.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh9_19173/09_2024/8rh9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh9_19173/09_2024/8rh9_19173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh9_19173/09_2024/8rh9_19173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh9_19173/09_2024/8rh9_19173.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh9_19173/09_2024/8rh9_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.40, per 1000 atoms: 0.66 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: 3.51 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: 1.67 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: 4.37 Time building geometry restraints manager: 3.95 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: 6.810 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.300 Find NCS groups from input model: 0.790 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- 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 : 0.003 0.072 14568 Z= 0.207 Angle : 0.637 8.219 19673 Z= 0.308 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 1.552 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: 0.3047 time to fit residues: 128.8820 Evaluate side-chains 214 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 14568 Z= 0.209 Angle : 0.543 6.023 19673 Z= 0.296 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8865 (mmtp) REVERT: A 181 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7589 (mt0) REVERT: A 227 MET cc_start: 0.7281 (ttt) cc_final: 0.6949 (ttm) REVERT: A 372 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7573 (tp40) REVERT: B 76 GLU cc_start: 0.7107 (mp0) cc_final: 0.6841 (mp0) REVERT: B 181 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7900 (mt0) REVERT: B 223 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 225 ASP cc_start: 0.8211 (m-30) cc_final: 0.7949 (m-30) REVERT: C 88 MET cc_start: 0.7278 (ptp) cc_final: 0.6774 (ptm) REVERT: C 170 ASP cc_start: 0.8546 (p0) cc_final: 0.8328 (p0) REVERT: C 179 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.6933 (ttm-80) REVERT: C 304 TRP cc_start: 0.8566 (m100) cc_final: 0.8207 (m-90) REVERT: C 373 GLU cc_start: 0.6766 (mm-30) cc_final: 0.5638 (mt-10) REVERT: D 84 HIS cc_start: 0.7556 (m90) cc_final: 0.7294 (m90) REVERT: D 111 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 149 LEU cc_start: 0.9016 (tp) cc_final: 0.8790 (tt) REVERT: E 83 ASP cc_start: 0.8000 (m-30) cc_final: 0.7465 (t70) REVERT: E 84 HIS cc_start: 0.7241 (m90) cc_final: 0.6543 (m90) REVERT: E 117 ASP cc_start: 0.8837 (p0) cc_final: 0.8619 (p0) REVERT: E 179 ARG cc_start: 0.7187 (ttp-170) cc_final: 0.6852 (ttm-80) REVERT: E 181 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6961 (mp10) outliers start: 39 outliers final: 28 residues processed: 246 average time/residue: 0.2991 time to fit residues: 104.4700 Evaluate side-chains 242 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 ASN D 274 ASN E 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14568 Z= 0.281 Angle : 0.557 5.677 19673 Z= 0.305 Chirality : 0.042 0.157 2213 Planarity : 0.004 0.058 2381 Dihedral : 6.820 131.032 2308 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.78 % Allowed : 8.09 % 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: 1.47 (0.21), residues: 1645 helix: 1.97 (0.22), residues: 570 sheet: 0.89 (0.23), residues: 445 loop : 0.22 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 349 HIS 0.006 0.001 HIS D 254 PHE 0.020 0.002 PHE C 356 TYR 0.017 0.002 TYR D 272 ARG 0.007 0.000 ARG E 278 *********************** 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 252 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8853 (mmtp) REVERT: A 181 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7582 (mt0) REVERT: B 76 GLU cc_start: 0.7179 (mp0) cc_final: 0.6900 (mp0) REVERT: B 181 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7871 (mt0) REVERT: B 223 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8041 (tp30) REVERT: C 76 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7610 (pm20) REVERT: C 88 MET cc_start: 0.7313 (ptp) cc_final: 0.6819 (ptm) REVERT: C 179 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.6939 (ttm-80) REVERT: D 84 HIS cc_start: 0.7595 (m90) cc_final: 0.7365 (m90) REVERT: D 149 LEU cc_start: 0.9055 (tp) cc_final: 0.8831 (tt) REVERT: E 83 ASP cc_start: 0.8014 (m-30) cc_final: 0.7523 (t70) REVERT: E 84 HIS cc_start: 0.7260 (m90) cc_final: 0.6550 (m90) REVERT: E 117 ASP cc_start: 0.8887 (p0) cc_final: 0.8647 (p0) REVERT: E 179 ARG cc_start: 0.7200 (ttp-170) cc_final: 0.6858 (ttm-80) REVERT: E 181 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.6856 (mp10) outliers start: 43 outliers final: 33 residues processed: 233 average time/residue: 0.2800 time to fit residues: 94.0045 Evaluate side-chains 225 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** D 199 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14568 Z= 0.220 Angle : 0.510 5.029 19673 Z= 0.280 Chirality : 0.041 0.153 2213 Planarity : 0.004 0.047 2381 Dihedral : 6.636 128.256 2308 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.65 % Allowed : 9.26 % Favored : 88.09 % 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: 1.62 (0.21), residues: 1645 helix: 2.37 (0.22), residues: 535 sheet: 0.91 (0.25), residues: 405 loop : 0.25 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.005 0.001 HIS D 254 PHE 0.016 0.001 PHE A 356 TYR 0.016 0.002 TYR D 272 ARG 0.002 0.000 ARG E 278 *********************** 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 237 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8847 (mmtp) REVERT: A 181 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7566 (mt0) REVERT: B 181 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7865 (mt0) REVERT: B 223 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 76 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7614 (pm20) REVERT: C 88 MET cc_start: 0.7348 (ptp) cc_final: 0.6851 (ptm) REVERT: C 143 MET cc_start: 0.7858 (mtm) cc_final: 0.7565 (mtt) REVERT: C 179 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.6915 (ttm-80) REVERT: D 111 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8264 (mt) REVERT: D 149 LEU cc_start: 0.9065 (tp) cc_final: 0.8848 (tt) REVERT: E 83 ASP cc_start: 0.8022 (m-30) cc_final: 0.7582 (t70) REVERT: E 84 HIS cc_start: 0.7274 (m90) cc_final: 0.6557 (m90) REVERT: E 117 ASP cc_start: 0.8847 (p0) cc_final: 0.8637 (p0) REVERT: E 179 ARG cc_start: 0.7129 (ttp-170) cc_final: 0.6750 (ttm-80) REVERT: E 181 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6756 (mp10) outliers start: 41 outliers final: 30 residues processed: 220 average time/residue: 0.3386 time to fit residues: 107.6418 Evaluate side-chains 218 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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 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 C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 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 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 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** D 199 ASN E 234 ASN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14568 Z= 0.238 Angle : 0.520 5.643 19673 Z= 0.285 Chirality : 0.041 0.154 2213 Planarity : 0.004 0.064 2381 Dihedral : 6.650 126.847 2308 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.65 % Allowed : 10.74 % Favored : 86.60 % 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: 1.56 (0.21), residues: 1645 helix: 2.35 (0.22), residues: 535 sheet: 0.86 (0.25), residues: 405 loop : 0.19 (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 0.016 0.001 PHE C 356 TYR 0.016 0.002 TYR D 272 ARG 0.004 0.000 ARG C 242 *********************** 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 228 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8850 (mmtp) REVERT: A 181 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7537 (mt0) REVERT: B 181 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7834 (mt0) REVERT: C 76 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7619 (pm20) REVERT: C 88 MET cc_start: 0.7359 (ptp) cc_final: 0.6858 (ptm) REVERT: C 143 MET cc_start: 0.7845 (mtm) cc_final: 0.7576 (mtt) REVERT: C 179 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.6895 (ttm-80) REVERT: C 223 GLU cc_start: 0.7985 (pt0) cc_final: 0.7781 (pm20) REVERT: D 149 LEU cc_start: 0.9057 (tp) cc_final: 0.8845 (tt) REVERT: E 83 ASP cc_start: 0.8030 (m-30) cc_final: 0.7618 (t70) REVERT: E 84 HIS cc_start: 0.7237 (m90) cc_final: 0.6507 (m90) REVERT: E 117 ASP cc_start: 0.8859 (p0) cc_final: 0.8657 (p0) REVERT: E 179 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6759 (ttm-80) REVERT: E 181 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6798 (mp10) outliers start: 41 outliers final: 36 residues processed: 211 average time/residue: 0.2804 time to fit residues: 85.5493 Evaluate side-chains 215 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 C 332 ASN D 287 GLN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14568 Z= 0.159 Angle : 0.470 4.990 19673 Z= 0.258 Chirality : 0.040 0.146 2213 Planarity : 0.004 0.061 2381 Dihedral : 6.334 124.932 2308 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.52 % Allowed : 11.07 % Favored : 86.41 % 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: 2.46 (0.22), residues: 535 sheet: 0.97 (0.25), residues: 405 loop : 0.24 (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 0.023 0.001 PHE E 92 TYR 0.016 0.001 TYR D 340 ARG 0.003 0.000 ARG C 242 *********************** 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 230 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8844 (mmtp) REVERT: A 181 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7497 (mt0) REVERT: B 181 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7961 (mt0) REVERT: B 282 PHE cc_start: 0.7759 (m-80) cc_final: 0.7537 (m-10) REVERT: C 76 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7617 (pm20) REVERT: C 88 MET cc_start: 0.7367 (ptp) cc_final: 0.6868 (ptm) REVERT: C 143 MET cc_start: 0.7748 (mtm) cc_final: 0.7515 (mtt) REVERT: C 179 ARG cc_start: 0.7422 (ttp-170) cc_final: 0.6889 (ttm-80) REVERT: C 223 GLU cc_start: 0.7889 (pt0) cc_final: 0.7563 (pm20) REVERT: C 308 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7802 (ttm110) REVERT: D 111 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8216 (mt) REVERT: D 149 LEU cc_start: 0.8999 (tp) cc_final: 0.8785 (tt) REVERT: E 83 ASP cc_start: 0.8066 (m-30) cc_final: 0.7678 (t70) REVERT: E 84 HIS cc_start: 0.7225 (m90) cc_final: 0.6472 (m90) REVERT: E 117 ASP cc_start: 0.8807 (p0) cc_final: 0.8586 (p0) REVERT: E 151 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8532 (mmtm) REVERT: E 179 ARG cc_start: 0.7111 (ttp-170) cc_final: 0.6724 (ttm-80) REVERT: E 181 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.6696 (mp10) REVERT: E 251 GLN cc_start: 0.8345 (pt0) cc_final: 0.8001 (pm20) outliers start: 39 outliers final: 30 residues processed: 213 average time/residue: 0.2731 time to fit residues: 84.8694 Evaluate side-chains 214 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 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 C residue 108 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 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 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 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 153 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 0.0040 chunk 96 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14568 Z= 0.191 Angle : 0.486 5.001 19673 Z= 0.266 Chirality : 0.040 0.148 2213 Planarity : 0.004 0.070 2381 Dihedral : 6.311 124.408 2308 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.91 % Allowed : 11.00 % 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: 1.68 (0.21), residues: 1645 helix: 2.47 (0.22), residues: 535 sheet: 0.96 (0.25), residues: 405 loop : 0.22 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.036 0.001 PHE E 92 TYR 0.015 0.001 TYR D 340 ARG 0.003 0.000 ARG C 242 *********************** 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 231 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8837 (mmtp) REVERT: A 181 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7474 (mt0) REVERT: B 181 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7987 (mt0) REVERT: B 282 PHE cc_start: 0.7765 (m-80) cc_final: 0.7542 (m-10) REVERT: C 76 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7612 (pm20) REVERT: C 88 MET cc_start: 0.7344 (ptp) cc_final: 0.6856 (ptm) REVERT: C 143 MET cc_start: 0.7755 (mtm) cc_final: 0.7509 (mtt) REVERT: C 179 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.6897 (ttm-80) REVERT: C 308 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7794 (ttm110) REVERT: D 111 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8235 (mt) REVERT: D 149 LEU cc_start: 0.9004 (tp) cc_final: 0.8788 (tt) REVERT: E 83 ASP cc_start: 0.8051 (m-30) cc_final: 0.7680 (t70) REVERT: E 84 HIS cc_start: 0.7227 (m90) cc_final: 0.6493 (m90) REVERT: E 117 ASP cc_start: 0.8797 (p0) cc_final: 0.8582 (p0) REVERT: E 179 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6729 (ttm-80) REVERT: E 181 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: E 251 GLN cc_start: 0.8368 (pt0) cc_final: 0.7991 (pm20) outliers start: 45 outliers final: 37 residues processed: 211 average time/residue: 0.2757 time to fit residues: 84.4137 Evaluate side-chains 219 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 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 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 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 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 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 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN C 332 ASN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14568 Z= 0.166 Angle : 0.475 4.974 19673 Z= 0.260 Chirality : 0.040 0.146 2213 Planarity : 0.004 0.061 2381 Dihedral : 6.194 123.894 2308 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.59 % Allowed : 11.20 % 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: 1.73 (0.21), residues: 1645 helix: 2.51 (0.22), residues: 535 sheet: 0.99 (0.26), residues: 405 loop : 0.25 (0.23), 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 0.015 0.001 TYR D 340 ARG 0.003 0.000 ARG C 242 *********************** 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 223 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8846 (mmtp) REVERT: A 181 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7468 (mt0) REVERT: B 181 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7989 (mt0) REVERT: B 282 PHE cc_start: 0.7768 (m-80) cc_final: 0.7551 (m-10) REVERT: C 76 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7617 (pm20) REVERT: C 143 MET cc_start: 0.7748 (mtm) cc_final: 0.7537 (mtt) REVERT: C 179 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.6870 (ttm-80) REVERT: C 308 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7759 (ttm110) REVERT: D 111 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8218 (mt) REVERT: D 149 LEU cc_start: 0.8976 (tp) cc_final: 0.8759 (tt) REVERT: E 83 ASP cc_start: 0.8061 (m-30) cc_final: 0.7686 (t70) REVERT: E 84 HIS cc_start: 0.7225 (m90) cc_final: 0.6468 (m90) REVERT: E 117 ASP cc_start: 0.8775 (p0) cc_final: 0.8557 (p0) REVERT: E 179 ARG cc_start: 0.7108 (ttp-170) cc_final: 0.6713 (ttm-80) REVERT: E 181 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: E 251 GLN cc_start: 0.8351 (pt0) cc_final: 0.7966 (pm20) outliers start: 40 outliers final: 31 residues processed: 207 average time/residue: 0.2972 time to fit residues: 89.8126 Evaluate side-chains 209 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 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 190 LEU 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 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 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 152 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14568 Z= 0.160 Angle : 0.471 4.991 19673 Z= 0.258 Chirality : 0.040 0.145 2213 Planarity : 0.004 0.073 2381 Dihedral : 6.088 123.447 2308 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.27 % Allowed : 11.52 % 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: 1.76 (0.21), residues: 1645 helix: 2.53 (0.22), residues: 535 sheet: 1.01 (0.26), residues: 405 loop : 0.26 (0.24), 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 0.033 0.001 PHE E 92 TYR 0.016 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 *********************** 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 217 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8853 (mmtp) REVERT: A 181 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7475 (mt0) REVERT: B 181 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7887 (mt0) REVERT: B 282 PHE cc_start: 0.7781 (m-80) cc_final: 0.7562 (m-10) REVERT: C 76 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7583 (pm20) REVERT: C 143 MET cc_start: 0.7743 (mtm) cc_final: 0.7516 (mtt) REVERT: C 179 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.6895 (ttm-80) REVERT: C 287 GLN cc_start: 0.7184 (mm110) cc_final: 0.6961 (mm-40) REVERT: C 308 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7761 (ttm110) REVERT: D 111 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8189 (mt) REVERT: D 149 LEU cc_start: 0.8968 (tp) cc_final: 0.8750 (tt) REVERT: E 83 ASP cc_start: 0.8053 (m-30) cc_final: 0.7681 (t70) REVERT: E 84 HIS cc_start: 0.7247 (m90) cc_final: 0.6495 (m90) REVERT: E 117 ASP cc_start: 0.8769 (p0) cc_final: 0.8550 (p0) REVERT: E 179 ARG cc_start: 0.7064 (ttp-170) cc_final: 0.6739 (ttm-80) REVERT: E 181 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6692 (mp10) outliers start: 35 outliers final: 32 residues processed: 202 average time/residue: 0.2700 time to fit residues: 78.9064 Evaluate side-chains 209 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 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 190 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14568 Z= 0.187 Angle : 0.489 6.102 19673 Z= 0.267 Chirality : 0.040 0.149 2213 Planarity : 0.004 0.074 2381 Dihedral : 6.102 123.032 2308 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.20 % Allowed : 11.52 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.51 (0.22), residues: 535 sheet: 1.00 (0.26), residues: 405 loop : 0.22 (0.23), 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 0.014 0.001 PHE E 92 TYR 0.015 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 ********************** 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 214 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8857 (mmtp) REVERT: A 181 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7483 (mt0) REVERT: B 181 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7992 (mt0) REVERT: B 282 PHE cc_start: 0.7778 (m-80) cc_final: 0.7559 (m-10) REVERT: C 143 MET cc_start: 0.7729 (mtm) cc_final: 0.7510 (mtt) REVERT: C 179 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.6892 (ttm-80) REVERT: C 308 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7805 (ttm110) REVERT: D 111 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8228 (mt) REVERT: D 149 LEU cc_start: 0.8971 (tp) cc_final: 0.8750 (tt) REVERT: E 83 ASP cc_start: 0.8060 (m-30) cc_final: 0.7698 (t70) REVERT: E 84 HIS cc_start: 0.7252 (m90) cc_final: 0.6482 (m90) REVERT: E 117 ASP cc_start: 0.8785 (p0) cc_final: 0.8578 (p0) REVERT: E 179 ARG cc_start: 0.7080 (ttp-170) cc_final: 0.6744 (ttm-80) REVERT: E 181 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.6679 (mp10) outliers start: 34 outliers final: 32 residues processed: 199 average time/residue: 0.2840 time to fit residues: 81.1554 Evaluate side-chains 209 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 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 190 LEU 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 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 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 139 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.131806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100468 restraints weight = 18793.946| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.41 r_work: 0.2955 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14568 Z= 0.147 Angle : 0.463 5.171 19673 Z= 0.253 Chirality : 0.039 0.149 2213 Planarity : 0.004 0.073 2381 Dihedral : 5.921 121.847 2308 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.01 % Allowed : 11.84 % Favored : 86.15 % 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: 1.81 (0.21), residues: 1645 helix: 2.57 (0.22), residues: 535 sheet: 1.07 (0.26), residues: 405 loop : 0.27 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.003 0.001 HIS A 254 PHE 0.010 0.001 PHE C 356 TYR 0.016 0.001 TYR D 340 ARG 0.004 0.000 ARG C 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.27 seconds wall clock time: 63 minutes 21.32 seconds (3801.32 seconds total)