Starting phenix.real_space_refine on Fri Jul 3 06:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngc_49382/07_2026/9ngc_49382_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngc_49382/07_2026/9ngc_49382.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/9ngc_49382/07_2026/9ngc_49382_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2026/9ngc_49382_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2026/9ngc_49382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2026/9ngc_49382.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= -0.000 sd= 0.131 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 25 5.16 5 Na 2 4.78 5 C 8305 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12722 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "C" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "E" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12722 At special positions: 0 Unit cell: (91.14, 93.744, 124.992, 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 25 16.00 Na 2 11.00 O 2275 8.00 N 2115 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 493.2 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 36.8% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.842A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 227 through 244 removed outlier: 3.627A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.635A pdb=" N ASN A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 298 through 301 removed outlier: 4.183A pdb=" N ARG A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 302 through 320 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.842A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 244 removed outlier: 3.627A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.635A pdb=" N ASN B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 298 through 301 removed outlier: 4.183A pdb=" N ARG B 301 " --> pdb=" O GLN B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 302 through 320 Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.842A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 227 through 244 removed outlier: 3.627A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.635A pdb=" N ASN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 298 through 301 removed outlier: 4.183A pdb=" N ARG C 301 " --> pdb=" O GLN C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 302 through 320 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.843A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.627A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.634A pdb=" N ASN D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 298 through 301 removed outlier: 4.183A pdb=" N ARG D 301 " --> pdb=" O GLN D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 302 through 320 Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.843A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 227 through 244 removed outlier: 3.627A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.635A pdb=" N ASN E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 298 through 301 removed outlier: 4.183A pdb=" N ARG E 301 " --> pdb=" O GLN E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 302 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.364A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.574A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.364A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.574A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.364A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.574A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.364A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.574A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.363A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.575A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.745A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3688 1.34 - 1.45: 2308 1.45 - 1.57: 7019 1.57 - 1.69: 5 1.69 - 1.80: 45 Bond restraints: 13065 Sorted by residual: bond pdb=" C PHE D 304 " pdb=" N PRO D 305 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.18e+00 bond pdb=" C PHE E 304 " pdb=" N PRO E 305 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.17e+00 bond pdb=" C PHE A 304 " pdb=" N PRO A 305 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.15e+00 bond pdb=" C PHE B 304 " pdb=" N PRO B 305 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.13e+00 bond pdb=" C PHE C 304 " pdb=" N PRO C 305 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.23e-02 6.61e+03 2.11e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 17044 1.53 - 3.05: 576 3.05 - 4.58: 95 4.58 - 6.11: 35 6.11 - 7.63: 30 Bond angle restraints: 17780 Sorted by residual: angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 ... (remaining 17775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.15: 6517 12.15 - 24.29: 808 24.29 - 36.44: 210 36.44 - 48.59: 60 48.59 - 60.73: 10 Dihedral angle restraints: 7605 sinusoidal: 3060 harmonic: 4545 Sorted by residual: dihedral pdb=" CA ILE D 157 " pdb=" C ILE D 157 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " ideal model delta harmonic sigma weight residual 180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ILE A 157 " pdb=" C ILE A 157 " pdb=" N ASP A 158 " pdb=" CA ASP A 158 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ILE C 157 " pdb=" C ILE C 157 " pdb=" N ASP C 158 " pdb=" CA ASP C 158 " ideal model delta harmonic sigma weight residual 180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 7602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1428 0.049 - 0.097: 373 0.097 - 0.146: 134 0.146 - 0.194: 15 0.194 - 0.243: 5 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CB THR B 149 " pdb=" CA THR B 149 " pdb=" OG1 THR B 149 " pdb=" CG2 THR B 149 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB THR A 149 " pdb=" CA THR A 149 " pdb=" OG1 THR A 149 " pdb=" CG2 THR A 149 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB THR E 149 " pdb=" CA THR E 149 " pdb=" OG1 THR E 149 " pdb=" CG2 THR E 149 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1952 not shown) Planarity restraints: 2265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 54 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO B 55 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 54 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 55 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 54 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO E 55 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.028 5.00e-02 4.00e+02 ... (remaining 2262 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1811 2.76 - 3.30: 11025 3.30 - 3.83: 20891 3.83 - 4.37: 24391 4.37 - 4.90: 43952 Nonbonded interactions: 102070 Sorted by model distance: nonbonded pdb=" OG SER D 229 " pdb=" OE2 GLU E 230 " model vdw 2.227 3.040 nonbonded pdb=" OG SER C 229 " pdb=" OE2 GLU D 230 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 229 " pdb=" OE2 GLU B 230 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 230 " pdb=" OG SER E 229 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 229 " pdb=" OE2 GLU C 230 " model vdw 2.265 3.040 ... (remaining 102065 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 11 through 401) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.090 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.004 0.041 13065 Z= 0.185 Angle : 0.728 7.632 17780 Z= 0.381 Chirality : 0.050 0.243 1955 Planarity : 0.005 0.050 2265 Dihedral : 11.953 60.734 4675 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1540 helix: -0.60 (0.20), residues: 565 sheet: 1.40 (0.25), residues: 465 loop : -2.16 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 91 TYR 0.009 0.001 TYR B 203 PHE 0.011 0.002 PHE E 116 TRP 0.020 0.002 TRP C 206 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (13065) covalent geometry : angle 0.72810 / 0.38 (17780) hydrogen bonds : bond 0.15258 / 10.06 ( 600) hydrogen bonds : angle 6.85309 / 4.78 ( 1995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.392 Fit side-chains REVERT: A 36 ASP cc_start: 0.8021 (t0) cc_final: 0.7726 (t70) REVERT: A 155 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6675 (mm-30) REVERT: A 176 ASP cc_start: 0.7778 (m-30) cc_final: 0.7555 (m-30) REVERT: A 187 GLU cc_start: 0.7446 (tt0) cc_final: 0.7181 (tt0) REVERT: B 34 LYS cc_start: 0.8301 (mttm) cc_final: 0.8091 (mttp) REVERT: B 36 ASP cc_start: 0.8020 (t0) cc_final: 0.7656 (t70) REVERT: B 61 THR cc_start: 0.8208 (t) cc_final: 0.7807 (p) REVERT: B 69 ASN cc_start: 0.7815 (m-40) cc_final: 0.7601 (m-40) REVERT: B 90 LYS cc_start: 0.8336 (pttt) cc_final: 0.7839 (ptpp) REVERT: B 155 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6692 (mm-30) REVERT: C 27 ASN cc_start: 0.8271 (t0) cc_final: 0.8044 (t0) REVERT: C 36 ASP cc_start: 0.8036 (t0) cc_final: 0.7614 (t0) REVERT: C 61 THR cc_start: 0.8176 (t) cc_final: 0.7742 (p) REVERT: C 90 LYS cc_start: 0.8308 (pttt) cc_final: 0.7826 (ptpp) REVERT: C 155 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6665 (mm-30) REVERT: C 187 GLU cc_start: 0.7660 (tt0) cc_final: 0.7405 (tt0) REVERT: C 233 GLN cc_start: 0.6719 (pt0) cc_final: 0.6490 (pt0) REVERT: D 34 LYS cc_start: 0.8255 (mttm) cc_final: 0.8024 (mttp) REVERT: D 36 ASP cc_start: 0.8109 (t0) cc_final: 0.7887 (t70) REVERT: D 90 LYS cc_start: 0.8440 (pttt) cc_final: 0.7937 (ptpp) REVERT: D 150 GLU cc_start: 0.7664 (pm20) cc_final: 0.7405 (mp0) REVERT: D 155 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6711 (mm-30) REVERT: D 176 ASP cc_start: 0.7708 (m-30) cc_final: 0.7425 (m-30) REVERT: D 233 GLN cc_start: 0.6844 (pt0) cc_final: 0.6618 (pt0) REVERT: E 36 ASP cc_start: 0.7960 (t0) cc_final: 0.7660 (t70) REVERT: E 61 THR cc_start: 0.8127 (t) cc_final: 0.7689 (p) REVERT: E 155 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6632 (mm-30) REVERT: E 233 GLN cc_start: 0.7002 (pt0) cc_final: 0.6725 (pt0) REVERT: E 239 MET cc_start: 0.7824 (ttp) cc_final: 0.7565 (ttp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.6016 time to fit residues: 122.6791 Evaluate side-chains 140 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 146 GLN A 184 ASN B 27 ASN B 42 GLN B 146 GLN C 42 GLN D 42 GLN E 27 ASN E 42 GLN E 146 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119480 restraints weight = 14346.541| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.18 r_work: 0.3342 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13065 Z= 0.147 Angle : 0.544 5.619 17780 Z= 0.287 Chirality : 0.045 0.137 1955 Planarity : 0.004 0.043 2265 Dihedral : 4.496 19.402 1715 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.37 % Allowed : 7.15 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.22), residues: 1540 helix: 0.73 (0.23), residues: 530 sheet: 1.33 (0.25), residues: 470 loop : -2.06 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.008 0.001 TYR A 204 PHE 0.010 0.001 PHE C 304 TRP 0.014 0.001 TRP B 206 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13065) covalent geometry : angle 0.54408 / 0.29 (17780) hydrogen bonds : bond 0.03626 / 2.37 ( 600) hydrogen bonds : angle 4.68681 / 3.24 ( 1995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.459 Fit side-chains REVERT: A 150 GLU cc_start: 0.7774 (pm20) cc_final: 0.7441 (mp0) REVERT: A 155 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6847 (mm-30) REVERT: A 156 GLU cc_start: 0.7736 (tt0) cc_final: 0.7396 (tt0) REVERT: A 176 ASP cc_start: 0.7965 (m-30) cc_final: 0.7636 (m-30) REVERT: A 187 GLU cc_start: 0.7607 (tt0) cc_final: 0.7380 (mt-10) REVERT: B 27 ASN cc_start: 0.8266 (t0) cc_final: 0.7864 (t0) REVERT: B 90 LYS cc_start: 0.8363 (pttt) cc_final: 0.7910 (ptpp) REVERT: B 93 MET cc_start: 0.8674 (ttm) cc_final: 0.8248 (mtp) REVERT: B 150 GLU cc_start: 0.7779 (pm20) cc_final: 0.7254 (mp0) REVERT: B 155 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6545 (mm-30) REVERT: B 156 GLU cc_start: 0.7673 (tt0) cc_final: 0.7326 (tt0) REVERT: C 27 ASN cc_start: 0.8250 (t0) cc_final: 0.8004 (t0) REVERT: C 90 LYS cc_start: 0.8291 (pttt) cc_final: 0.7746 (ptpp) REVERT: C 150 GLU cc_start: 0.7699 (pm20) cc_final: 0.7312 (mp0) REVERT: C 155 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6836 (mm-30) REVERT: D 27 ASN cc_start: 0.8090 (t0) cc_final: 0.7337 (t0) REVERT: D 34 LYS cc_start: 0.8328 (mttm) cc_final: 0.8128 (mmtp) REVERT: D 90 LYS cc_start: 0.8425 (pttt) cc_final: 0.7828 (ptpp) REVERT: D 93 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: D 150 GLU cc_start: 0.7623 (pm20) cc_final: 0.7243 (mp0) REVERT: D 155 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6884 (mm-30) REVERT: D 176 ASP cc_start: 0.7898 (m-30) cc_final: 0.7533 (m-30) REVERT: D 233 GLN cc_start: 0.6616 (pt0) cc_final: 0.6368 (tt0) REVERT: E 93 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8318 (mtp) REVERT: E 155 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6886 (mm-30) REVERT: E 174 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: E 239 MET cc_start: 0.7697 (ttp) cc_final: 0.7490 (ttp) outliers start: 19 outliers final: 6 residues processed: 170 average time/residue: 0.7102 time to fit residues: 129.2885 Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 184 ASN A 233 GLN B 42 GLN C 42 GLN D 42 GLN E 27 ASN E 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118020 restraints weight = 14399.950| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.17 r_work: 0.3319 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13065 Z= 0.149 Angle : 0.524 5.511 17780 Z= 0.274 Chirality : 0.045 0.141 1955 Planarity : 0.004 0.042 2265 Dihedral : 4.379 18.613 1715 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 9.39 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1540 helix: 1.15 (0.23), residues: 530 sheet: 1.60 (0.27), residues: 435 loop : -2.05 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 91 TYR 0.007 0.001 TYR D 148 PHE 0.010 0.001 PHE B 116 TRP 0.021 0.001 TRP C 206 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (13065) covalent geometry : angle 0.52355 / 0.27 (17780) hydrogen bonds : bond 0.03362 / 2.20 ( 600) hydrogen bonds : angle 4.47378 / 3.10 ( 1995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.483 Fit side-chains REVERT: A 150 GLU cc_start: 0.7850 (pm20) cc_final: 0.7434 (mp0) REVERT: A 155 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6867 (mm-30) REVERT: A 156 GLU cc_start: 0.7795 (tt0) cc_final: 0.7364 (tt0) REVERT: A 176 ASP cc_start: 0.8025 (m-30) cc_final: 0.7686 (m-30) REVERT: A 187 GLU cc_start: 0.7695 (tt0) cc_final: 0.7383 (mt-10) REVERT: B 27 ASN cc_start: 0.8092 (t0) cc_final: 0.7737 (t0) REVERT: B 69 ASN cc_start: 0.7453 (m-40) cc_final: 0.7197 (m-40) REVERT: B 90 LYS cc_start: 0.8372 (pttt) cc_final: 0.7884 (ptpp) REVERT: B 93 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: B 150 GLU cc_start: 0.7809 (pm20) cc_final: 0.7272 (mp0) REVERT: B 155 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6668 (mm-30) REVERT: B 156 GLU cc_start: 0.7752 (tt0) cc_final: 0.7381 (tt0) REVERT: C 27 ASN cc_start: 0.8280 (t0) cc_final: 0.8073 (t0) REVERT: C 29 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7680 (tt) REVERT: C 36 ASP cc_start: 0.8882 (t0) cc_final: 0.8579 (t70) REVERT: C 90 LYS cc_start: 0.8209 (pttt) cc_final: 0.7673 (ptpp) REVERT: C 150 GLU cc_start: 0.7753 (pm20) cc_final: 0.7313 (mp0) REVERT: C 155 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6812 (mm-30) REVERT: C 159 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6769 (pt0) REVERT: D 34 LYS cc_start: 0.8345 (mttm) cc_final: 0.8119 (mttp) REVERT: D 90 LYS cc_start: 0.8383 (pttt) cc_final: 0.7801 (ptpp) REVERT: D 93 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: D 150 GLU cc_start: 0.7714 (pm20) cc_final: 0.7247 (mp0) REVERT: D 155 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6769 (mm-30) REVERT: D 159 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: D 163 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7028 (mmt90) REVERT: D 174 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: D 176 ASP cc_start: 0.7972 (m-30) cc_final: 0.7642 (m-30) REVERT: D 187 GLU cc_start: 0.7496 (tt0) cc_final: 0.7283 (mt-10) REVERT: E 36 ASP cc_start: 0.8791 (t0) cc_final: 0.8531 (t70) REVERT: E 93 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8328 (mtp) REVERT: E 155 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6883 (mm-30) REVERT: E 185 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: E 239 MET cc_start: 0.7563 (ttp) cc_final: 0.7358 (ttp) outliers start: 17 outliers final: 6 residues processed: 168 average time/residue: 0.6709 time to fit residues: 120.8839 Evaluate side-chains 169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 184 ASN A 233 GLN B 233 GLN E 27 ASN E 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120426 restraints weight = 14399.987| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.18 r_work: 0.3355 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13065 Z= 0.105 Angle : 0.478 5.261 17780 Z= 0.249 Chirality : 0.044 0.141 1955 Planarity : 0.003 0.041 2265 Dihedral : 4.136 18.051 1715 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.44 % Allowed : 11.05 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1540 helix: 1.37 (0.23), residues: 530 sheet: 1.74 (0.27), residues: 435 loop : -2.01 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 163 TYR 0.005 0.001 TYR B 203 PHE 0.008 0.001 PHE C 116 TRP 0.023 0.001 TRP C 206 HIS 0.002 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13065) covalent geometry : angle 0.47797 / 0.25 (17780) hydrogen bonds : bond 0.02841 / 1.86 ( 600) hydrogen bonds : angle 4.21026 / 2.92 ( 1995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.470 Fit side-chains REVERT: A 36 ASP cc_start: 0.8893 (t0) cc_final: 0.8481 (t70) REVERT: A 150 GLU cc_start: 0.7832 (pm20) cc_final: 0.7458 (mp0) REVERT: A 155 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6870 (mm-30) REVERT: A 156 GLU cc_start: 0.7843 (tt0) cc_final: 0.7424 (tt0) REVERT: B 27 ASN cc_start: 0.8090 (t0) cc_final: 0.7682 (t0) REVERT: B 69 ASN cc_start: 0.7456 (m-40) cc_final: 0.7202 (m-40) REVERT: B 90 LYS cc_start: 0.8365 (pttt) cc_final: 0.7848 (ptpp) REVERT: B 93 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: B 137 ASN cc_start: 0.7344 (p0) cc_final: 0.7077 (p0) REVERT: B 150 GLU cc_start: 0.7794 (pm20) cc_final: 0.7239 (mp0) REVERT: B 155 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6737 (mm-30) REVERT: B 156 GLU cc_start: 0.7760 (tt0) cc_final: 0.7351 (tt0) REVERT: B 163 ARG cc_start: 0.7319 (mmt90) cc_final: 0.7007 (mmp80) REVERT: B 174 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7579 (ttm-80) REVERT: C 27 ASN cc_start: 0.8238 (t0) cc_final: 0.7960 (t0) REVERT: C 29 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7656 (tt) REVERT: C 90 LYS cc_start: 0.8216 (pttt) cc_final: 0.7616 (ptpp) REVERT: C 93 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8279 (mtp) REVERT: C 137 ASN cc_start: 0.7320 (p0) cc_final: 0.7086 (p0) REVERT: C 150 GLU cc_start: 0.7679 (pm20) cc_final: 0.7322 (mp0) REVERT: C 155 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6812 (mm-30) REVERT: D 27 ASN cc_start: 0.8067 (t0) cc_final: 0.7496 (t0) REVERT: D 34 LYS cc_start: 0.8315 (mttm) cc_final: 0.8071 (mttp) REVERT: D 90 LYS cc_start: 0.8330 (pttt) cc_final: 0.7829 (ptpp) REVERT: D 93 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8315 (mtp) REVERT: D 150 GLU cc_start: 0.7649 (pm20) cc_final: 0.7208 (mp0) REVERT: D 155 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6731 (mm-30) REVERT: D 159 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: D 163 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7046 (mmp80) REVERT: D 176 ASP cc_start: 0.7980 (m-30) cc_final: 0.7647 (m-30) REVERT: E 93 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: E 155 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6744 (mm-30) REVERT: E 185 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: E 239 MET cc_start: 0.7540 (ttp) cc_final: 0.7339 (ttp) outliers start: 20 outliers final: 9 residues processed: 172 average time/residue: 0.6543 time to fit residues: 120.8771 Evaluate side-chains 172 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 135 optimal weight: 0.0570 chunk 140 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN D 146 GLN E 27 ASN E 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119629 restraints weight = 14347.207| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.10 r_work: 0.3342 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13065 Z= 0.122 Angle : 0.493 5.336 17780 Z= 0.257 Chirality : 0.044 0.136 1955 Planarity : 0.003 0.040 2265 Dihedral : 4.079 17.856 1715 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.02 % Allowed : 11.55 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1540 helix: 1.47 (0.23), residues: 530 sheet: 1.76 (0.27), residues: 435 loop : -1.97 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.006 0.001 TYR D 148 PHE 0.009 0.001 PHE B 116 TRP 0.024 0.001 TRP C 206 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13065) covalent geometry : angle 0.49258 / 0.26 (17780) hydrogen bonds : bond 0.02911 / 1.91 ( 600) hydrogen bonds : angle 4.18002 / 2.91 ( 1995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.379 Fit side-chains REVERT: A 155 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6789 (mm-30) REVERT: A 156 GLU cc_start: 0.7861 (tt0) cc_final: 0.7413 (tt0) REVERT: B 36 ASP cc_start: 0.8965 (t0) cc_final: 0.8736 (t70) REVERT: B 69 ASN cc_start: 0.7411 (m-40) cc_final: 0.7166 (m-40) REVERT: B 90 LYS cc_start: 0.8330 (pttt) cc_final: 0.7813 (ptpp) REVERT: B 93 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: B 155 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6669 (mm-30) REVERT: B 156 GLU cc_start: 0.7739 (tt0) cc_final: 0.7306 (tt0) REVERT: B 163 ARG cc_start: 0.7406 (mmt90) cc_final: 0.7144 (mmp80) REVERT: C 29 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7657 (tt) REVERT: C 34 LYS cc_start: 0.8334 (mttm) cc_final: 0.7909 (mttm) REVERT: C 36 ASP cc_start: 0.8895 (t0) cc_final: 0.8555 (t70) REVERT: C 90 LYS cc_start: 0.8173 (pttt) cc_final: 0.7637 (ptpp) REVERT: C 93 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: C 137 ASN cc_start: 0.7399 (p0) cc_final: 0.7132 (p0) REVERT: C 150 GLU cc_start: 0.7740 (pm20) cc_final: 0.7343 (mp0) REVERT: C 155 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6728 (mm-30) REVERT: D 27 ASN cc_start: 0.8010 (t0) cc_final: 0.7333 (t0) REVERT: D 34 LYS cc_start: 0.8296 (mttm) cc_final: 0.8026 (mmtp) REVERT: D 36 ASP cc_start: 0.8844 (t0) cc_final: 0.8519 (t70) REVERT: D 86 ASP cc_start: 0.7678 (t70) cc_final: 0.7381 (t0) REVERT: D 90 LYS cc_start: 0.8277 (pttt) cc_final: 0.7781 (ptpp) REVERT: D 93 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: D 150 GLU cc_start: 0.7718 (pm20) cc_final: 0.7301 (mp0) REVERT: D 155 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6804 (mm-30) REVERT: D 163 ARG cc_start: 0.7383 (mmt90) cc_final: 0.7055 (mmp80) REVERT: D 176 ASP cc_start: 0.7965 (m-30) cc_final: 0.7631 (m-30) REVERT: D 304 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5929 (t80) REVERT: E 36 ASP cc_start: 0.8803 (t0) cc_final: 0.8582 (t70) REVERT: E 93 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8345 (mtp) REVERT: E 155 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6675 (mm-30) REVERT: E 185 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7330 (pt0) outliers start: 28 outliers final: 14 residues processed: 167 average time/residue: 0.5962 time to fit residues: 107.6017 Evaluate side-chains 169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 221 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 152 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 0.0050 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 143 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120551 restraints weight = 14294.656| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.15 r_work: 0.3362 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13065 Z= 0.102 Angle : 0.470 5.220 17780 Z= 0.245 Chirality : 0.044 0.137 1955 Planarity : 0.003 0.040 2265 Dihedral : 3.935 17.611 1715 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.59 % Allowed : 13.00 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1540 helix: 1.57 (0.23), residues: 530 sheet: 1.83 (0.27), residues: 435 loop : -1.95 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.006 0.001 TYR B 203 PHE 0.008 0.001 PHE A 116 TRP 0.025 0.001 TRP C 206 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (13065) covalent geometry : angle 0.46993 / 0.25 (17780) hydrogen bonds : bond 0.02665 / 1.75 ( 600) hydrogen bonds : angle 4.05737 / 2.82 ( 1995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.475 Fit side-chains REVERT: A 36 ASP cc_start: 0.8863 (t0) cc_final: 0.8493 (t70) REVERT: A 150 GLU cc_start: 0.7780 (pm20) cc_final: 0.7479 (mp0) REVERT: A 155 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6815 (mm-30) REVERT: A 156 GLU cc_start: 0.7856 (tt0) cc_final: 0.7504 (tt0) REVERT: B 27 ASN cc_start: 0.7939 (t0) cc_final: 0.7684 (t0) REVERT: B 69 ASN cc_start: 0.7443 (m-40) cc_final: 0.7191 (m-40) REVERT: B 90 LYS cc_start: 0.8338 (pttt) cc_final: 0.7810 (ptpp) REVERT: B 93 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: B 137 ASN cc_start: 0.7407 (p0) cc_final: 0.7152 (p0) REVERT: B 150 GLU cc_start: 0.7744 (pm20) cc_final: 0.7211 (mp0) REVERT: B 155 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6630 (mm-30) REVERT: B 156 GLU cc_start: 0.7732 (tt0) cc_final: 0.7317 (tt0) REVERT: B 163 ARG cc_start: 0.7337 (mmt90) cc_final: 0.7097 (mmp80) REVERT: C 29 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7697 (tt) REVERT: C 34 LYS cc_start: 0.8376 (mttm) cc_final: 0.7939 (mttm) REVERT: C 90 LYS cc_start: 0.8199 (pttt) cc_final: 0.7687 (ptpp) REVERT: C 93 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (mtp) REVERT: C 137 ASN cc_start: 0.7404 (p0) cc_final: 0.7159 (p0) REVERT: C 150 GLU cc_start: 0.7694 (pm20) cc_final: 0.7312 (mp0) REVERT: C 155 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6700 (mm-30) REVERT: D 27 ASN cc_start: 0.8050 (t0) cc_final: 0.7466 (t0) REVERT: D 34 LYS cc_start: 0.8310 (mttm) cc_final: 0.8057 (mmtp) REVERT: D 86 ASP cc_start: 0.7728 (t70) cc_final: 0.7440 (t0) REVERT: D 90 LYS cc_start: 0.8265 (pttt) cc_final: 0.7749 (ptpp) REVERT: D 93 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (mtp) REVERT: D 150 GLU cc_start: 0.7705 (pm20) cc_final: 0.7292 (mp0) REVERT: D 155 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6816 (mm-30) REVERT: D 159 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: D 163 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6992 (mmp80) REVERT: E 34 LYS cc_start: 0.8369 (mttm) cc_final: 0.8154 (mmtp) REVERT: E 93 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8380 (mtp) REVERT: E 150 GLU cc_start: 0.7779 (pm20) cc_final: 0.7325 (mp0) REVERT: E 155 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6798 (mm-30) REVERT: E 156 GLU cc_start: 0.7681 (tt0) cc_final: 0.7310 (tt0) REVERT: E 185 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7383 (pt0) outliers start: 22 outliers final: 11 residues processed: 171 average time/residue: 0.6409 time to fit residues: 117.8185 Evaluate side-chains 166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 152 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN B 27 ASN E 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118379 restraints weight = 14287.364| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.10 r_work: 0.3349 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13065 Z= 0.132 Angle : 0.497 5.319 17780 Z= 0.261 Chirality : 0.045 0.132 1955 Planarity : 0.004 0.040 2265 Dihedral : 4.066 18.229 1715 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.17 % Allowed : 13.29 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.22), residues: 1540 helix: 1.58 (0.23), residues: 530 sheet: 1.78 (0.27), residues: 435 loop : -1.94 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.007 0.001 TYR E 204 PHE 0.010 0.001 PHE C 116 TRP 0.026 0.001 TRP C 206 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13065) covalent geometry : angle 0.49692 / 0.26 (17780) hydrogen bonds : bond 0.02918 / 1.92 ( 600) hydrogen bonds : angle 4.16182 / 2.90 ( 1995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8887 (t0) cc_final: 0.8522 (t70) REVERT: A 69 ASN cc_start: 0.7511 (m-40) cc_final: 0.7298 (m-40) REVERT: A 150 GLU cc_start: 0.7792 (pm20) cc_final: 0.7460 (mp0) REVERT: A 155 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6877 (mm-30) REVERT: A 156 GLU cc_start: 0.7894 (tt0) cc_final: 0.7442 (tt0) REVERT: B 36 ASP cc_start: 0.8966 (t0) cc_final: 0.8533 (t70) REVERT: B 69 ASN cc_start: 0.7443 (m-40) cc_final: 0.7198 (m-40) REVERT: B 90 LYS cc_start: 0.8362 (pttt) cc_final: 0.7826 (ptpp) REVERT: B 93 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: B 137 ASN cc_start: 0.7489 (p0) cc_final: 0.7134 (p0) REVERT: B 155 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6668 (mm-30) REVERT: B 156 GLU cc_start: 0.7750 (tt0) cc_final: 0.7313 (tt0) REVERT: B 163 ARG cc_start: 0.7460 (mmt90) cc_final: 0.7178 (mmp80) REVERT: B 174 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7586 (ttm-80) REVERT: C 90 LYS cc_start: 0.8214 (pttt) cc_final: 0.7632 (ptpp) REVERT: C 93 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8298 (mtp) REVERT: C 137 ASN cc_start: 0.7494 (p0) cc_final: 0.7171 (p0) REVERT: C 150 GLU cc_start: 0.7760 (pm20) cc_final: 0.7347 (mp0) REVERT: C 155 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6725 (mm-30) REVERT: C 159 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6666 (pt0) REVERT: D 27 ASN cc_start: 0.8091 (t0) cc_final: 0.7461 (t0) REVERT: D 34 LYS cc_start: 0.8347 (mttm) cc_final: 0.8087 (mmtp) REVERT: D 36 ASP cc_start: 0.8918 (t0) cc_final: 0.8585 (t70) REVERT: D 86 ASP cc_start: 0.7775 (t70) cc_final: 0.7495 (t0) REVERT: D 90 LYS cc_start: 0.8285 (pttt) cc_final: 0.7790 (ptpp) REVERT: D 93 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: D 155 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6910 (mm-30) REVERT: D 159 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7028 (pt0) REVERT: D 163 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7090 (mmp80) REVERT: E 36 ASP cc_start: 0.8852 (t0) cc_final: 0.8608 (t70) REVERT: E 93 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: E 155 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6880 (mm-30) REVERT: E 185 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7416 (pt0) outliers start: 30 outliers final: 17 residues processed: 161 average time/residue: 0.6075 time to fit residues: 105.2638 Evaluate side-chains 168 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 5.9990 chunk 85 optimal weight: 0.0070 chunk 74 optimal weight: 0.0000 chunk 154 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121457 restraints weight = 14335.548| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.12 r_work: 0.3366 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13065 Z= 0.106 Angle : 0.473 5.332 17780 Z= 0.247 Chirality : 0.044 0.133 1955 Planarity : 0.003 0.040 2265 Dihedral : 3.951 17.814 1715 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.81 % Allowed : 13.79 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1540 helix: 1.65 (0.23), residues: 530 sheet: 1.83 (0.27), residues: 435 loop : -1.95 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.006 0.001 TYR B 203 PHE 0.009 0.001 PHE C 116 TRP 0.028 0.001 TRP C 206 HIS 0.002 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13065) covalent geometry : angle 0.47264 / 0.25 (17780) hydrogen bonds : bond 0.02679 / 1.76 ( 600) hydrogen bonds : angle 4.06225 / 2.83 ( 1995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.472 Fit side-chains REVERT: A 36 ASP cc_start: 0.8878 (t0) cc_final: 0.8495 (t70) REVERT: A 150 GLU cc_start: 0.7762 (pm20) cc_final: 0.7456 (mp0) REVERT: A 155 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6876 (mm-30) REVERT: A 156 GLU cc_start: 0.7880 (tt0) cc_final: 0.7441 (tt0) REVERT: A 163 ARG cc_start: 0.7234 (mmt90) cc_final: 0.7012 (mmt90) REVERT: B 69 ASN cc_start: 0.7449 (m-40) cc_final: 0.7200 (m-40) REVERT: B 90 LYS cc_start: 0.8348 (pttt) cc_final: 0.7832 (ptpp) REVERT: B 93 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: B 137 ASN cc_start: 0.7466 (p0) cc_final: 0.7200 (p0) REVERT: B 155 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6648 (mm-30) REVERT: B 156 GLU cc_start: 0.7772 (tt0) cc_final: 0.7344 (tt0) REVERT: B 163 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7153 (mmp80) REVERT: B 174 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7576 (ttm-80) REVERT: C 34 LYS cc_start: 0.8401 (mttm) cc_final: 0.7981 (mttm) REVERT: C 90 LYS cc_start: 0.8241 (pttt) cc_final: 0.7664 (ptpp) REVERT: C 93 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: C 137 ASN cc_start: 0.7419 (p0) cc_final: 0.7172 (p0) REVERT: C 150 GLU cc_start: 0.7694 (pm20) cc_final: 0.7301 (mp0) REVERT: C 155 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6761 (mm-30) REVERT: C 163 ARG cc_start: 0.7379 (mmt90) cc_final: 0.7145 (mmt90) REVERT: D 27 ASN cc_start: 0.8086 (t0) cc_final: 0.7469 (t0) REVERT: D 34 LYS cc_start: 0.8319 (mttm) cc_final: 0.8065 (mmtp) REVERT: D 86 ASP cc_start: 0.7797 (t70) cc_final: 0.7527 (t0) REVERT: D 90 LYS cc_start: 0.8244 (pttt) cc_final: 0.7718 (ptpp) REVERT: D 93 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: D 155 GLU cc_start: 0.7644 (mt-10) cc_final: 0.6880 (mm-30) REVERT: D 159 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: D 163 ARG cc_start: 0.7313 (mmt90) cc_final: 0.7019 (mmp80) REVERT: E 36 ASP cc_start: 0.8787 (t0) cc_final: 0.8544 (t70) REVERT: E 93 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (mtp) REVERT: E 155 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6838 (mm-30) REVERT: E 163 ARG cc_start: 0.7364 (mmt90) cc_final: 0.7127 (mmt90) REVERT: E 185 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7450 (pt0) outliers start: 25 outliers final: 15 residues processed: 163 average time/residue: 0.5753 time to fit residues: 101.3652 Evaluate side-chains 169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 117 optimal weight: 0.0070 chunk 147 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121791 restraints weight = 14399.824| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.13 r_work: 0.3381 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13065 Z= 0.103 Angle : 0.468 5.276 17780 Z= 0.244 Chirality : 0.044 0.132 1955 Planarity : 0.003 0.040 2265 Dihedral : 3.907 18.362 1715 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.31 % Allowed : 13.57 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1540 helix: 1.69 (0.23), residues: 530 sheet: 1.84 (0.27), residues: 435 loop : -1.92 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 163 TYR 0.006 0.001 TYR B 203 PHE 0.008 0.001 PHE D 116 TRP 0.031 0.001 TRP C 206 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (13065) covalent geometry : angle 0.46756 / 0.24 (17780) hydrogen bonds : bond 0.02627 / 1.73 ( 600) hydrogen bonds : angle 4.01587 / 2.80 ( 1995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.290 Fit side-chains REVERT: A 36 ASP cc_start: 0.8870 (t0) cc_final: 0.8492 (t70) REVERT: A 150 GLU cc_start: 0.7809 (pm20) cc_final: 0.7490 (mp0) REVERT: A 155 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6860 (mm-30) REVERT: A 156 GLU cc_start: 0.7888 (tt0) cc_final: 0.7492 (tt0) REVERT: B 27 ASN cc_start: 0.8158 (t0) cc_final: 0.7830 (t0) REVERT: B 69 ASN cc_start: 0.7447 (m-40) cc_final: 0.7187 (m-40) REVERT: B 90 LYS cc_start: 0.8328 (pttt) cc_final: 0.7857 (ptpp) REVERT: B 93 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: B 137 ASN cc_start: 0.7492 (p0) cc_final: 0.7233 (p0) REVERT: B 155 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6634 (mm-30) REVERT: B 156 GLU cc_start: 0.7790 (tt0) cc_final: 0.7359 (tt0) REVERT: B 163 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7127 (mmp80) REVERT: B 174 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7571 (ttm-80) REVERT: C 34 LYS cc_start: 0.8377 (mttm) cc_final: 0.7968 (mttm) REVERT: C 90 LYS cc_start: 0.8223 (pttt) cc_final: 0.7656 (ptpp) REVERT: C 93 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8332 (mtp) REVERT: C 137 ASN cc_start: 0.7403 (p0) cc_final: 0.7185 (p0) REVERT: C 150 GLU cc_start: 0.7725 (pm20) cc_final: 0.7318 (mp0) REVERT: C 155 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6732 (mm-30) REVERT: D 27 ASN cc_start: 0.8076 (t0) cc_final: 0.7456 (t0) REVERT: D 34 LYS cc_start: 0.8326 (mttm) cc_final: 0.8077 (mmtp) REVERT: D 86 ASP cc_start: 0.7790 (t70) cc_final: 0.7523 (t0) REVERT: D 90 LYS cc_start: 0.8189 (pttt) cc_final: 0.7671 (ptpp) REVERT: D 93 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (mtp) REVERT: D 150 GLU cc_start: 0.7760 (pm20) cc_final: 0.7243 (mp0) REVERT: D 155 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6839 (mm-30) REVERT: D 156 GLU cc_start: 0.7671 (tt0) cc_final: 0.7343 (tp30) REVERT: D 159 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: D 163 ARG cc_start: 0.7326 (mmt90) cc_final: 0.7045 (mmp80) REVERT: E 27 ASN cc_start: 0.8023 (t0) cc_final: 0.7783 (t0) REVERT: E 93 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8399 (mtp) REVERT: E 150 GLU cc_start: 0.7782 (pm20) cc_final: 0.7342 (mp0) REVERT: E 155 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6823 (mm-30) REVERT: E 156 GLU cc_start: 0.7727 (tt0) cc_final: 0.7347 (tt0) REVERT: E 185 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7448 (pt0) outliers start: 32 outliers final: 17 residues processed: 178 average time/residue: 0.5971 time to fit residues: 114.4798 Evaluate side-chains 172 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN E 21 ASN E 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116663 restraints weight = 14370.648| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.16 r_work: 0.3334 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13065 Z= 0.153 Angle : 0.513 5.415 17780 Z= 0.269 Chirality : 0.045 0.134 1955 Planarity : 0.004 0.039 2265 Dihedral : 4.143 18.880 1715 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.31 % Allowed : 13.72 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1540 helix: 1.63 (0.23), residues: 530 sheet: 1.75 (0.27), residues: 435 loop : -1.95 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.007 0.001 TYR A 204 PHE 0.010 0.001 PHE C 116 TRP 0.032 0.002 TRP C 206 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (13065) covalent geometry : angle 0.51285 / 0.27 (17780) hydrogen bonds : bond 0.03021 / 1.98 ( 600) hydrogen bonds : angle 4.21560 / 2.94 ( 1995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.469 Fit side-chains REVERT: A 36 ASP cc_start: 0.8876 (t0) cc_final: 0.8504 (t70) REVERT: A 69 ASN cc_start: 0.7525 (m-40) cc_final: 0.7320 (m-40) REVERT: A 150 GLU cc_start: 0.7837 (pm20) cc_final: 0.7490 (mp0) REVERT: A 155 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6898 (mm-30) REVERT: A 156 GLU cc_start: 0.7842 (tt0) cc_final: 0.7457 (tt0) REVERT: B 36 ASP cc_start: 0.9041 (t0) cc_final: 0.8595 (t70) REVERT: B 69 ASN cc_start: 0.7463 (m-40) cc_final: 0.7194 (m-40) REVERT: B 90 LYS cc_start: 0.8348 (pttt) cc_final: 0.7832 (ptpp) REVERT: B 93 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: B 137 ASN cc_start: 0.7540 (p0) cc_final: 0.7190 (p0) REVERT: B 155 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6729 (mm-30) REVERT: B 156 GLU cc_start: 0.7821 (tt0) cc_final: 0.7461 (tt0) REVERT: B 163 ARG cc_start: 0.7438 (mmt90) cc_final: 0.7193 (mmp80) REVERT: C 36 ASP cc_start: 0.8920 (t0) cc_final: 0.8520 (t70) REVERT: C 90 LYS cc_start: 0.8195 (pttt) cc_final: 0.7645 (ptpp) REVERT: C 137 ASN cc_start: 0.7525 (p0) cc_final: 0.7215 (p0) REVERT: C 150 GLU cc_start: 0.7785 (pm20) cc_final: 0.7350 (mp0) REVERT: C 155 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6801 (mm-30) REVERT: D 34 LYS cc_start: 0.8340 (mttm) cc_final: 0.8083 (mmtp) REVERT: D 36 ASP cc_start: 0.8925 (t0) cc_final: 0.8452 (t70) REVERT: D 69 ASN cc_start: 0.7452 (m-40) cc_final: 0.7201 (m-40) REVERT: D 86 ASP cc_start: 0.7790 (t70) cc_final: 0.7505 (t0) REVERT: D 90 LYS cc_start: 0.8300 (pttt) cc_final: 0.7801 (ptpp) REVERT: D 93 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: D 150 GLU cc_start: 0.7882 (pm20) cc_final: 0.7376 (mp0) REVERT: D 155 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6824 (mm-30) REVERT: D 156 GLU cc_start: 0.7728 (tt0) cc_final: 0.7428 (tp30) REVERT: D 163 ARG cc_start: 0.7404 (mmt90) cc_final: 0.7094 (mmp80) REVERT: E 36 ASP cc_start: 0.8845 (t0) cc_final: 0.8569 (t70) REVERT: E 93 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: E 155 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6894 (mm-30) REVERT: E 174 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7674 (ttm-80) REVERT: E 185 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7400 (pt0) outliers start: 32 outliers final: 20 residues processed: 164 average time/residue: 0.6162 time to fit residues: 109.4113 Evaluate side-chains 168 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 109 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 233 GLN E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119481 restraints weight = 14265.240| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.15 r_work: 0.3371 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13065 Z= 0.101 Angle : 0.472 5.311 17780 Z= 0.247 Chirality : 0.044 0.133 1955 Planarity : 0.003 0.040 2265 Dihedral : 3.927 18.150 1715 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.02 % Allowed : 13.94 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1540 helix: 1.71 (0.23), residues: 530 sheet: 1.83 (0.27), residues: 435 loop : -1.95 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 163 TYR 0.007 0.001 TYR B 203 PHE 0.008 0.001 PHE D 116 TRP 0.034 0.001 TRP C 206 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (13065) covalent geometry : angle 0.47228 / 0.25 (17780) hydrogen bonds : bond 0.02605 / 1.71 ( 600) hydrogen bonds : angle 4.04141 / 2.82 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3794.41 seconds wall clock time: 65 minutes 25.35 seconds (3925.35 seconds total)