Starting phenix.real_space_refine on Tue May 5 02:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yi4_72977/05_2026/9yi4_72977_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yi4_72977/05_2026/9yi4_72977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yi4_72977/05_2026/9yi4_72977_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yi4_72977/05_2026/9yi4_72977_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yi4_72977/05_2026/9yi4_72977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yi4_72977/05_2026/9yi4_72977.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 80 5.16 5 C 8100 2.51 5 N 1865 2.21 5 O 2300 1.98 5 H 11950 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24295 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "B" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "C" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "D" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "E" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {'NAG': 5, 'STR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {'NAG': 5, 'STR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {'NAG': 5, 'STR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {'NAG': 5, 'STR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {'NAG': 5, 'STR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.52, per 1000 atoms: 0.19 Number of scatterers: 24295 At special positions: 0 Unit cell: (94.86, 96.72, 121.83, 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) S 80 16.00 O 2300 8.00 N 1865 7.00 C 8100 6.00 H 11950 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 150 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 150 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 150 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 150 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 145 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 77 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 180 " " NAG A 404 " - " ASN A 186 " " NAG A 405 " - " ASN A 17 " " NAG B 401 " - " ASN B 77 " " NAG B 402 " - " ASN B 27 " " NAG B 403 " - " ASN B 180 " " NAG B 404 " - " ASN B 186 " " NAG B 405 " - " ASN B 17 " " NAG C 401 " - " ASN C 77 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 180 " " NAG C 404 " - " ASN C 186 " " NAG C 405 " - " ASN C 17 " " NAG D 401 " - " ASN D 77 " " NAG D 402 " - " ASN D 27 " " NAG D 403 " - " ASN D 180 " " NAG D 404 " - " ASN D 186 " " NAG D 405 " - " ASN D 17 " " NAG E 402 " - " ASN E 77 " " NAG E 403 " - " ASN E 27 " " NAG E 404 " - " ASN E 180 " " NAG E 405 " - " ASN E 186 " " NAG E 406 " - " ASN E 17 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 561.1 milliseconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2810 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 20 sheets defined 33.2% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.144A pdb=" N ASN A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 206 through 229 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 235 through 258 removed outlier: 3.538A pdb=" N THR A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 292 Processing helix chain 'B' and resid 3 through 15 Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.140A pdb=" N ASN B 76 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 206 through 229 Proline residue: B 215 - end of helix Processing helix chain 'B' and resid 235 through 258 Processing helix chain 'B' and resid 266 through 292 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 71 through 76 removed outlier: 4.130A pdb=" N ASN C 76 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 206 through 229 Proline residue: C 215 - end of helix Processing helix chain 'C' and resid 235 through 258 removed outlier: 3.548A pdb=" N THR C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 292 Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.123A pdb=" N ASN D 76 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.927A pdb=" N ILE D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 229 Proline residue: D 215 - end of helix Processing helix chain 'D' and resid 235 through 258 removed outlier: 3.544A pdb=" N THR D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 292 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.149A pdb=" N ASN E 76 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 229 Proline residue: E 215 - end of helix Processing helix chain 'E' and resid 235 through 258 removed outlier: 3.538A pdb=" N THR E 257 " --> pdb=" O GLN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.927A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 63 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.927A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 63 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 52 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP A 45 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET A 54 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 43 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 56 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE A 64 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 33 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA A 36 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 164 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A 38 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 166 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 40 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP A 168 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N THR A 42 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.156A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.156A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 3.910A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 63 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 84 removed outlier: 3.910A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 63 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE B 52 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP B 45 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET B 54 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU B 43 " --> pdb=" O MET B 54 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 56 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE B 64 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 33 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 32 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS B 162 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 34 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 164 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 36 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR B 166 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 38 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP B 168 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 40 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.547A pdb=" N LYS B 94 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.547A pdb=" N LYS B 94 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.951A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 63 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.951A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 63 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE C 52 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP C 45 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET C 54 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU C 43 " --> pdb=" O MET C 54 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG C 56 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE C 64 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP C 33 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL C 32 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LYS C 162 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 34 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 164 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA C 36 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR C 166 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 38 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP C 168 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 40 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 removed outlier: 5.278A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 94 removed outlier: 5.278A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.928A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 63 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.928A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 63 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE D 52 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP D 45 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET D 54 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU D 43 " --> pdb=" O MET D 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG D 56 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE D 64 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP D 33 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 32 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 161 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 34 " --> pdb=" O ILE D 161 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 163 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 94 removed outlier: 5.180A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 5.180A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.920A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP E 63 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 129 " --> pdb=" O ILE E 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.920A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP E 63 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG E 56 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU E 43 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR E 58 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN E 41 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY E 60 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR E 39 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE E 62 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU E 37 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE E 64 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N THR E 35 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL E 32 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS E 162 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL E 34 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU E 164 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA E 36 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR E 166 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU E 38 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP E 168 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 40 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 removed outlier: 5.122A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 93 through 94 removed outlier: 5.122A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1950 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: 4.86 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11950 1.03 - 1.23: 72 1.23 - 1.43: 5060 1.43 - 1.63: 7378 1.63 - 1.83: 140 Bond restraints: 24600 Sorted by residual: bond pdb=" N THR B 1 " pdb=" CA THR B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N THR A 1 " pdb=" CA THR A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N THR D 1 " pdb=" CA THR D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N THR E 1 " pdb=" CA THR E 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" N THR C 1 " pdb=" CA THR C 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 24595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 41343 1.43 - 2.86: 2691 2.86 - 4.28: 295 4.28 - 5.71: 96 5.71 - 7.14: 5 Bond angle restraints: 44430 Sorted by residual: angle pdb=" CA ILE D 209 " pdb=" CB ILE D 209 " pdb=" CG2 ILE D 209 " ideal model delta sigma weight residual 110.50 116.18 -5.68 1.70e+00 3.46e-01 1.11e+01 angle pdb=" CA CYS A 96 " pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " ideal model delta sigma weight residual 114.40 107.26 7.14 2.30e+00 1.89e-01 9.64e+00 angle pdb=" CA CYS B 150 " pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " ideal model delta sigma weight residual 114.40 121.10 -6.70 2.30e+00 1.89e-01 8.48e+00 angle pdb=" CA ILE B 53 " pdb=" CB ILE B 53 " pdb=" CG1 ILE B 53 " ideal model delta sigma weight residual 110.40 114.89 -4.49 1.70e+00 3.46e-01 6.96e+00 angle pdb=" C ILE B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta sigma weight residual 120.42 116.75 3.67 1.42e+00 4.96e-01 6.68e+00 ... (remaining 44425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.58: 10328 12.58 - 25.17: 1220 25.17 - 37.75: 386 37.75 - 50.33: 187 50.33 - 62.92: 109 Dihedral angle restraints: 12230 sinusoidal: 6975 harmonic: 5255 Sorted by residual: dihedral pdb=" CA SER C 98 " pdb=" C SER C 98 " pdb=" N MET C 99 " pdb=" CA MET C 99 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER E 98 " pdb=" C SER E 98 " pdb=" N MET E 99 " pdb=" CA MET E 99 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASN D 97 " pdb=" C ASN D 97 " pdb=" N SER D 98 " pdb=" CA SER D 98 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 12227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1116 0.031 - 0.062: 628 0.062 - 0.093: 232 0.093 - 0.124: 109 0.124 - 0.155: 40 Chirality restraints: 2125 Sorted by residual: chirality pdb=" CA MET E 54 " pdb=" N MET E 54 " pdb=" C MET E 54 " pdb=" CB MET E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CG LEU C 46 " pdb=" CB LEU C 46 " pdb=" CD1 LEU C 46 " pdb=" CD2 LEU C 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CG LEU B 46 " pdb=" CB LEU B 46 " pdb=" CD1 LEU B 46 " pdb=" CD2 LEU B 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 2122 not shown) Planarity restraints: 3450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 214 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO B 215 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 214 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO E 215 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 215 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 215 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 214 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO A 215 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.036 5.00e-02 4.00e+02 ... (remaining 3447 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2056 2.23 - 2.82: 51948 2.82 - 3.42: 60607 3.42 - 4.01: 86556 4.01 - 4.60: 128994 Nonbonded interactions: 330161 Sorted by model distance: nonbonded pdb="HD22 ASN C 261 " pdb=" O ASN D 174 " model vdw 1.642 2.450 nonbonded pdb="HD22 ASN D 261 " pdb=" O ASN E 174 " model vdw 1.646 2.450 nonbonded pdb="HD22 ASN A 261 " pdb=" O ASN B 174 " model vdw 1.646 2.450 nonbonded pdb="HD22 ASN B 261 " pdb=" O ASN C 174 " model vdw 1.650 2.450 nonbonded pdb=" O ASN A 174 " pdb="HD22 ASN E 261 " model vdw 1.653 2.450 ... (remaining 330156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 292 or resid 402 through 405)) selection = (chain 'B' and (resid 1 through 292 or resid 402 through 405)) selection = (chain 'C' and (resid 1 through 292 or resid 402 through 405)) selection = (chain 'D' and (resid 1 through 292 or resid 402 through 405)) selection = (chain 'E' and (resid 1 through 292 or resid 402 through 405)) } 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: 2.000 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: 0.180 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.120 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12685 Z= 0.217 Angle : 0.824 7.140 17370 Z= 0.416 Chirality : 0.049 0.155 2125 Planarity : 0.006 0.072 2035 Dihedral : 13.398 62.915 5255 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1450 helix: 2.60 (0.24), residues: 430 sheet: -0.23 (0.24), residues: 420 loop : -0.61 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 125 TYR 0.017 0.001 TYR E 58 PHE 0.012 0.002 PHE A 227 TRP 0.009 0.001 TRP A 118 HIS 0.013 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00494 (12650) covalent geometry : angle 0.82113 (17275) SS BOND : bond 0.00918 ( 10) SS BOND : angle 1.38464 ( 20) hydrogen bonds : bond 0.14721 ( 585) hydrogen bonds : angle 5.47288 ( 1950) link_NAG-ASN : bond 0.00095 ( 25) link_NAG-ASN : angle 1.19135 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8108 (t0) cc_final: 0.7614 (p0) REVERT: A 97 ASN cc_start: 0.8493 (t0) cc_final: 0.8273 (t0) REVERT: A 244 PHE cc_start: 0.8706 (t80) cc_final: 0.8437 (t80) REVERT: A 274 LEU cc_start: 0.8198 (tt) cc_final: 0.7993 (tt) REVERT: A 277 MET cc_start: 0.8449 (tmm) cc_final: 0.8244 (tmm) REVERT: A 278 LEU cc_start: 0.9068 (tt) cc_final: 0.8724 (mm) REVERT: B 269 MET cc_start: 0.8796 (ttp) cc_final: 0.7935 (tmm) REVERT: B 277 MET cc_start: 0.8213 (tmm) cc_final: 0.7958 (tmm) REVERT: C 173 GLN cc_start: 0.8424 (mm110) cc_final: 0.8157 (mp10) REVERT: C 277 MET cc_start: 0.8209 (tmm) cc_final: 0.7936 (tmm) REVERT: D 244 PHE cc_start: 0.8595 (t80) cc_final: 0.8306 (t80) REVERT: D 270 LEU cc_start: 0.7456 (tt) cc_final: 0.7172 (tt) REVERT: D 277 MET cc_start: 0.8466 (tmm) cc_final: 0.8263 (tmm) REVERT: E 45 ASP cc_start: 0.7955 (t0) cc_final: 0.7707 (t0) outliers start: 0 outliers final: 1 residues processed: 164 average time/residue: 0.8755 time to fit residues: 161.5278 Evaluate side-chains 113 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 250 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 261 ASN D 51 ASN D 261 ASN E 128 HIS ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075831 restraints weight = 61595.117| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.89 r_work: 0.2863 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12685 Z= 0.151 Angle : 0.611 8.691 17370 Z= 0.312 Chirality : 0.042 0.150 2125 Planarity : 0.005 0.061 2035 Dihedral : 9.082 57.460 2412 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.10 % Allowed : 8.75 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1450 helix: 2.84 (0.23), residues: 430 sheet: -0.17 (0.23), residues: 420 loop : -0.42 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.009 0.001 TYR E 58 PHE 0.007 0.001 PHE C 244 TRP 0.006 0.001 TRP E 122 HIS 0.009 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00338 (12650) covalent geometry : angle 0.60391 (17275) SS BOND : bond 0.00634 ( 10) SS BOND : angle 1.70060 ( 20) hydrogen bonds : bond 0.04583 ( 585) hydrogen bonds : angle 4.46246 ( 1950) link_NAG-ASN : bond 0.00201 ( 25) link_NAG-ASN : angle 1.30506 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8284 (t0) cc_final: 0.7752 (p0) REVERT: A 97 ASN cc_start: 0.8588 (t0) cc_final: 0.8335 (t0) REVERT: A 190 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7095 (pp20) REVERT: B 244 PHE cc_start: 0.8512 (t80) cc_final: 0.8298 (t80) REVERT: B 269 MET cc_start: 0.8825 (ttp) cc_final: 0.7946 (tmm) REVERT: B 277 MET cc_start: 0.8082 (tmm) cc_final: 0.7841 (tmm) REVERT: C 173 GLN cc_start: 0.8524 (mm110) cc_final: 0.8192 (mp10) REVERT: C 190 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: C 277 MET cc_start: 0.8119 (tmm) cc_final: 0.7899 (tmm) outliers start: 15 outliers final: 2 residues processed: 126 average time/residue: 0.8071 time to fit residues: 115.3849 Evaluate side-chains 121 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 250 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.0040 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN B 51 ASN B 261 ASN D 51 ASN D 261 ASN E 51 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.076003 restraints weight = 61140.019| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.87 r_work: 0.2860 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12685 Z= 0.133 Angle : 0.557 6.330 17370 Z= 0.282 Chirality : 0.041 0.140 2125 Planarity : 0.005 0.060 2035 Dihedral : 8.437 58.184 2412 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.44 % Allowed : 10.37 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.22), residues: 1450 helix: 2.88 (0.23), residues: 430 sheet: -0.14 (0.23), residues: 425 loop : -0.36 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 56 TYR 0.008 0.001 TYR E 57 PHE 0.011 0.001 PHE C 244 TRP 0.006 0.001 TRP C 122 HIS 0.007 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00307 (12650) covalent geometry : angle 0.55051 (17275) SS BOND : bond 0.00457 ( 10) SS BOND : angle 1.46151 ( 20) hydrogen bonds : bond 0.03860 ( 585) hydrogen bonds : angle 4.14747 ( 1950) link_NAG-ASN : bond 0.00089 ( 25) link_NAG-ASN : angle 1.20978 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8254 (t0) cc_final: 0.7745 (p0) REVERT: A 97 ASN cc_start: 0.8663 (t0) cc_final: 0.8339 (t0) REVERT: A 190 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: A 278 LEU cc_start: 0.8876 (tm) cc_final: 0.8578 (mm) REVERT: B 244 PHE cc_start: 0.8516 (t80) cc_final: 0.8281 (t80) REVERT: B 269 MET cc_start: 0.8843 (ttp) cc_final: 0.7941 (tmm) REVERT: B 277 MET cc_start: 0.8083 (tmm) cc_final: 0.7861 (tmm) REVERT: C 173 GLN cc_start: 0.8497 (mm110) cc_final: 0.8182 (mp10) REVERT: C 190 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7292 (pp20) outliers start: 6 outliers final: 3 residues processed: 125 average time/residue: 0.8477 time to fit residues: 119.7588 Evaluate side-chains 124 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 134 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075890 restraints weight = 60975.326| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.87 r_work: 0.2854 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12685 Z= 0.132 Angle : 0.538 6.787 17370 Z= 0.272 Chirality : 0.041 0.137 2125 Planarity : 0.005 0.060 2035 Dihedral : 7.851 59.837 2412 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.59 % Allowed : 11.03 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1450 helix: 2.93 (0.23), residues: 430 sheet: -0.10 (0.23), residues: 425 loop : -0.40 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 56 TYR 0.007 0.001 TYR C 175 PHE 0.011 0.001 PHE C 244 TRP 0.005 0.001 TRP D 118 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00304 (12650) covalent geometry : angle 0.53141 (17275) SS BOND : bond 0.00423 ( 10) SS BOND : angle 1.28709 ( 20) hydrogen bonds : bond 0.03517 ( 585) hydrogen bonds : angle 3.99929 ( 1950) link_NAG-ASN : bond 0.00097 ( 25) link_NAG-ASN : angle 1.24530 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASN cc_start: 0.8691 (t0) cc_final: 0.8334 (t0) REVERT: A 190 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: B 244 PHE cc_start: 0.8570 (t80) cc_final: 0.8353 (t80) REVERT: B 269 MET cc_start: 0.8851 (ttp) cc_final: 0.7943 (tmm) REVERT: B 273 MET cc_start: 0.8328 (tmm) cc_final: 0.8114 (tmm) REVERT: B 277 MET cc_start: 0.8113 (tmm) cc_final: 0.7872 (tmm) REVERT: C 112 MET cc_start: 0.9363 (ttp) cc_final: 0.9117 (ttp) REVERT: C 173 GLN cc_start: 0.8580 (mm110) cc_final: 0.8225 (mp10) REVERT: C 190 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7236 (pp20) REVERT: E 45 ASP cc_start: 0.8178 (t0) cc_final: 0.7948 (t0) outliers start: 8 outliers final: 3 residues processed: 129 average time/residue: 0.8363 time to fit residues: 122.3642 Evaluate side-chains 122 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 14 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 51 ASN A 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.074473 restraints weight = 60689.295| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.84 r_work: 0.2830 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12685 Z= 0.173 Angle : 0.553 6.888 17370 Z= 0.277 Chirality : 0.041 0.131 2125 Planarity : 0.005 0.059 2035 Dihedral : 7.473 57.145 2412 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.81 % Allowed : 11.91 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1450 helix: 2.96 (0.23), residues: 430 sheet: -0.07 (0.23), residues: 425 loop : -0.41 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.007 0.001 TYR E 57 PHE 0.012 0.001 PHE C 244 TRP 0.007 0.001 TRP E 122 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00400 (12650) covalent geometry : angle 0.54647 (17275) SS BOND : bond 0.00446 ( 10) SS BOND : angle 1.12453 ( 20) hydrogen bonds : bond 0.03468 ( 585) hydrogen bonds : angle 3.96263 ( 1950) link_NAG-ASN : bond 0.00151 ( 25) link_NAG-ASN : angle 1.27372 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7222 (pp20) REVERT: B 244 PHE cc_start: 0.8586 (t80) cc_final: 0.8381 (t80) REVERT: B 269 MET cc_start: 0.8856 (ttp) cc_final: 0.8027 (tmm) REVERT: B 277 MET cc_start: 0.8144 (tmm) cc_final: 0.7910 (tmm) REVERT: C 173 GLN cc_start: 0.8560 (mm110) cc_final: 0.8227 (mp10) REVERT: C 190 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: E 45 ASP cc_start: 0.8131 (t0) cc_final: 0.7899 (t0) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 0.7919 time to fit residues: 114.2365 Evaluate side-chains 122 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN B 51 ASN B 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075327 restraints weight = 60531.436| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.86 r_work: 0.2846 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12685 Z= 0.120 Angle : 0.549 8.094 17370 Z= 0.273 Chirality : 0.040 0.136 2125 Planarity : 0.004 0.059 2035 Dihedral : 7.229 55.226 2412 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.96 % Allowed : 12.65 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1450 helix: 3.00 (0.23), residues: 430 sheet: -0.10 (0.23), residues: 425 loop : -0.42 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 160 TYR 0.007 0.001 TYR E 57 PHE 0.012 0.001 PHE C 244 TRP 0.005 0.001 TRP E 118 HIS 0.005 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00277 (12650) covalent geometry : angle 0.54209 (17275) SS BOND : bond 0.00465 ( 10) SS BOND : angle 1.54498 ( 20) hydrogen bonds : bond 0.03323 ( 585) hydrogen bonds : angle 3.88609 ( 1950) link_NAG-ASN : bond 0.00077 ( 25) link_NAG-ASN : angle 1.19305 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: B 244 PHE cc_start: 0.8582 (t80) cc_final: 0.8368 (t80) REVERT: B 269 MET cc_start: 0.8852 (ttp) cc_final: 0.8024 (tmm) REVERT: B 277 MET cc_start: 0.8163 (tmm) cc_final: 0.7924 (tmm) REVERT: C 173 GLN cc_start: 0.8555 (mm110) cc_final: 0.8208 (mp10) REVERT: C 190 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7230 (pp20) REVERT: D 173 GLN cc_start: 0.8343 (mp10) cc_final: 0.8053 (mp10) REVERT: E 45 ASP cc_start: 0.8107 (t0) cc_final: 0.7853 (t0) outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 0.8102 time to fit residues: 114.6185 Evaluate side-chains 126 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 173 GLN A 261 ASN B 51 ASN B 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073276 restraints weight = 60674.265| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.90 r_work: 0.2813 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12685 Z= 0.183 Angle : 0.572 8.095 17370 Z= 0.284 Chirality : 0.041 0.129 2125 Planarity : 0.005 0.059 2035 Dihedral : 7.032 54.510 2412 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.74 % Allowed : 12.94 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1450 helix: 3.02 (0.23), residues: 430 sheet: 0.04 (0.23), residues: 420 loop : -0.49 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.007 0.001 TYR E 57 PHE 0.013 0.001 PHE C 244 TRP 0.007 0.001 TRP E 122 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00429 (12650) covalent geometry : angle 0.56268 (17275) SS BOND : bond 0.00411 ( 10) SS BOND : angle 2.10238 ( 20) hydrogen bonds : bond 0.03390 ( 585) hydrogen bonds : angle 3.90025 ( 1950) link_NAG-ASN : bond 0.00186 ( 25) link_NAG-ASN : angle 1.29847 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: B 244 PHE cc_start: 0.8599 (t80) cc_final: 0.8389 (t80) REVERT: B 269 MET cc_start: 0.8867 (ttp) cc_final: 0.8030 (tmm) REVERT: B 277 MET cc_start: 0.8170 (tmm) cc_final: 0.7944 (tmm) REVERT: C 173 GLN cc_start: 0.8584 (mm110) cc_final: 0.8231 (mp10) REVERT: C 190 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7259 (pp20) REVERT: D 173 GLN cc_start: 0.8483 (mp10) cc_final: 0.8158 (mp10) REVERT: E 45 ASP cc_start: 0.8128 (t0) cc_final: 0.7874 (t0) outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 0.8313 time to fit residues: 117.7696 Evaluate side-chains 124 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 142 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN B 51 ASN B 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.110042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072302 restraints weight = 60606.363| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.88 r_work: 0.2809 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12685 Z= 0.182 Angle : 0.576 8.635 17370 Z= 0.286 Chirality : 0.041 0.131 2125 Planarity : 0.005 0.058 2035 Dihedral : 6.885 54.472 2412 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.81 % Allowed : 13.53 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.23), residues: 1450 helix: 2.98 (0.23), residues: 430 sheet: 0.03 (0.24), residues: 420 loop : -0.50 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.007 0.001 TYR E 57 PHE 0.013 0.001 PHE C 244 TRP 0.007 0.001 TRP B 122 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00422 (12650) covalent geometry : angle 0.56820 (17275) SS BOND : bond 0.00463 ( 10) SS BOND : angle 1.77303 ( 20) hydrogen bonds : bond 0.03395 ( 585) hydrogen bonds : angle 3.88297 ( 1950) link_NAG-ASN : bond 0.00128 ( 25) link_NAG-ASN : angle 1.24221 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: B 244 PHE cc_start: 0.8626 (t80) cc_final: 0.8384 (t80) REVERT: B 269 MET cc_start: 0.8881 (ttp) cc_final: 0.8081 (tmm) REVERT: B 277 MET cc_start: 0.8218 (tmm) cc_final: 0.7986 (tmm) REVERT: C 190 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: D 173 GLN cc_start: 0.8532 (mp10) cc_final: 0.8193 (mp10) REVERT: E 45 ASP cc_start: 0.8127 (t0) cc_final: 0.7871 (t0) outliers start: 11 outliers final: 5 residues processed: 122 average time/residue: 0.8481 time to fit residues: 116.9876 Evaluate side-chains 125 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 48 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 144 optimal weight: 10.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 173 GLN A 261 ASN B 51 ASN B 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.110854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073655 restraints weight = 60442.730| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.87 r_work: 0.2823 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12685 Z= 0.132 Angle : 0.561 8.909 17370 Z= 0.277 Chirality : 0.040 0.135 2125 Planarity : 0.004 0.059 2035 Dihedral : 6.716 54.469 2412 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.81 % Allowed : 13.82 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.22), residues: 1450 helix: 3.00 (0.23), residues: 430 sheet: 0.04 (0.24), residues: 420 loop : -0.46 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 160 TYR 0.006 0.001 TYR E 57 PHE 0.013 0.001 PHE C 244 TRP 0.006 0.001 TRP E 118 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00307 (12650) covalent geometry : angle 0.55514 (17275) SS BOND : bond 0.00359 ( 10) SS BOND : angle 1.54090 ( 20) hydrogen bonds : bond 0.03276 ( 585) hydrogen bonds : angle 3.80618 ( 1950) link_NAG-ASN : bond 0.00068 ( 25) link_NAG-ASN : angle 1.17551 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: B 244 PHE cc_start: 0.8612 (t80) cc_final: 0.8367 (t80) REVERT: B 269 MET cc_start: 0.8873 (ttp) cc_final: 0.8082 (tmm) REVERT: B 277 MET cc_start: 0.8225 (tmm) cc_final: 0.7995 (tmm) REVERT: C 190 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7242 (pp20) REVERT: D 173 GLN cc_start: 0.8528 (mp10) cc_final: 0.8205 (mp10) REVERT: D 225 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7816 (t80) REVERT: E 45 ASP cc_start: 0.8112 (t0) cc_final: 0.7857 (t0) outliers start: 11 outliers final: 4 residues processed: 123 average time/residue: 0.8613 time to fit residues: 119.8681 Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 22 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN B 51 ASN B 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079126 restraints weight = 61143.318| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.90 r_work: 0.2824 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12685 Z= 0.127 Angle : 0.558 9.199 17370 Z= 0.275 Chirality : 0.040 0.132 2125 Planarity : 0.004 0.059 2035 Dihedral : 6.606 54.108 2412 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.66 % Allowed : 14.49 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1450 helix: 3.03 (0.23), residues: 430 sheet: 0.04 (0.24), residues: 420 loop : -0.42 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 160 TYR 0.006 0.001 TYR E 57 PHE 0.015 0.001 PHE E 244 TRP 0.006 0.001 TRP D 122 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00297 (12650) covalent geometry : angle 0.55135 (17275) SS BOND : bond 0.00358 ( 10) SS BOND : angle 1.49054 ( 20) hydrogen bonds : bond 0.03220 ( 585) hydrogen bonds : angle 3.76255 ( 1950) link_NAG-ASN : bond 0.00063 ( 25) link_NAG-ASN : angle 1.18009 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: B 244 PHE cc_start: 0.8568 (t80) cc_final: 0.8301 (t80) REVERT: B 269 MET cc_start: 0.8863 (ttp) cc_final: 0.8074 (tmm) REVERT: C 190 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: C 227 PHE cc_start: 0.8623 (t80) cc_final: 0.8417 (t80) REVERT: D 173 GLN cc_start: 0.8538 (mp10) cc_final: 0.8205 (mp10) REVERT: D 225 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7801 (t80) REVERT: E 45 ASP cc_start: 0.8098 (t0) cc_final: 0.7846 (t0) outliers start: 9 outliers final: 4 residues processed: 124 average time/residue: 0.8699 time to fit residues: 121.7121 Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 173 GLN A 261 ASN B 51 ASN B 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.111446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074501 restraints weight = 60404.406| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.87 r_work: 0.2835 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12685 Z= 0.114 Angle : 0.558 9.421 17370 Z= 0.273 Chirality : 0.040 0.133 2125 Planarity : 0.004 0.057 2035 Dihedral : 6.521 53.865 2412 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.66 % Allowed : 14.56 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1450 helix: 3.03 (0.23), residues: 430 sheet: 0.07 (0.24), residues: 420 loop : -0.40 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.006 0.001 TYR E 57 PHE 0.013 0.001 PHE E 244 TRP 0.006 0.001 TRP D 122 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00268 (12650) covalent geometry : angle 0.55184 (17275) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.41633 ( 20) hydrogen bonds : bond 0.03169 ( 585) hydrogen bonds : angle 3.72537 ( 1950) link_NAG-ASN : bond 0.00065 ( 25) link_NAG-ASN : angle 1.14744 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7705.49 seconds wall clock time: 130 minutes 58.42 seconds (7858.42 seconds total)