Starting phenix.real_space_refine on Wed Feb 4 19:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngc_49382/02_2026/9ngc_49382_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngc_49382/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngc_49382/02_2026/9ngc_49382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngc_49382/02_2026/9ngc_49382.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngc_49382/02_2026/9ngc_49382_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngc_49382/02_2026/9ngc_49382_neut.cif" } 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-2.0-5952/lib/python3.9/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, 6 Unusual residues: {' NA': 2, '3CN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 3.17, per 1000 atoms: 0.25 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: 0.99 Conformation dependent library (CDL) restraints added in 606.1 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: 0.50 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: 2.30 Time building geometry restraints manager: 1.35 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: 1.600 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 covalent geometry : bond 0.00413 (13065) covalent geometry : angle 0.72810 (17780) hydrogen bonds : bond 0.15258 ( 600) hydrogen bonds : angle 6.85309 ( 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 : 0.480 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: 0.7078 time to fit residues: 143.7469 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 : 0.457 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7815 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 covalent geometry : bond 0.00344 (13065) covalent geometry : angle 0.54408 (17780) hydrogen bonds : bond 0.03626 ( 600) hydrogen bonds : angle 4.68681 ( 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 : 0.500 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: 0.7528 time to fit residues: 136.9006 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 : 0.485 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.151204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118062 restraints weight = 14399.842| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.17 r_work: 0.3319 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1455 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 5.508 17780 Z= 0.274 Chirality : 0.045 0.141 1955 Planarity : 0.004 0.042 2265 Dihedral : 4.379 18.626 1715 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.23 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: 0.24 (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 covalent geometry : bond 0.00353 (13065) covalent geometry : angle 0.52354 (17780) hydrogen bonds : bond 0.03362 ( 600) hydrogen bonds : angle 4.47425 ( 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 : 0.452 Fit side-chains REVERT: A 150 GLU cc_start: 0.7851 (pm20) cc_final: 0.7434 (mp0) REVERT: A 155 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6866 (mm-30) REVERT: A 156 GLU cc_start: 0.7796 (tt0) cc_final: 0.7364 (tt0) REVERT: A 176 ASP cc_start: 0.8024 (m-30) cc_final: 0.7686 (m-30) REVERT: A 187 GLU cc_start: 0.7695 (tt0) cc_final: 0.7384 (mt-10) REVERT: B 27 ASN cc_start: 0.8029 (t0) cc_final: 0.7665 (t0) REVERT: B 69 ASN cc_start: 0.7449 (m-40) cc_final: 0.7193 (m-40) REVERT: B 90 LYS cc_start: 0.8371 (pttt) cc_final: 0.7884 (ptpp) REVERT: B 93 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8180 (mtp) REVERT: B 150 GLU cc_start: 0.7809 (pm20) cc_final: 0.7272 (mp0) REVERT: B 155 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6667 (mm-30) REVERT: B 156 GLU cc_start: 0.7753 (tt0) cc_final: 0.7382 (tt0) REVERT: C 27 ASN cc_start: 0.8279 (t0) cc_final: 0.8071 (t0) REVERT: C 29 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7679 (tt) REVERT: C 36 ASP cc_start: 0.8883 (t0) cc_final: 0.8579 (t70) REVERT: C 90 LYS cc_start: 0.8208 (pttt) cc_final: 0.7672 (ptpp) REVERT: C 150 GLU cc_start: 0.7749 (pm20) cc_final: 0.7309 (mp0) REVERT: C 155 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6808 (mm-30) REVERT: C 159 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6779 (pt0) REVERT: D 34 LYS cc_start: 0.8345 (mttm) cc_final: 0.8120 (mttp) REVERT: D 90 LYS cc_start: 0.8383 (pttt) cc_final: 0.7800 (ptpp) REVERT: D 93 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (mtp) REVERT: D 150 GLU cc_start: 0.7712 (pm20) cc_final: 0.7245 (mp0) REVERT: D 155 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6767 (mm-30) REVERT: D 159 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: D 163 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7026 (mmt90) REVERT: D 174 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: D 176 ASP cc_start: 0.7971 (m-30) cc_final: 0.7640 (m-30) REVERT: D 187 GLU cc_start: 0.7495 (tt0) cc_final: 0.7283 (mt-10) REVERT: E 36 ASP cc_start: 0.8792 (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: 0.7292 (pt0) REVERT: E 239 MET cc_start: 0.7560 (ttp) cc_final: 0.7356 (ttp) outliers start: 17 outliers final: 6 residues processed: 168 average time/residue: 0.7222 time to fit residues: 130.0741 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 : 0.475 ------------------------------------------------------------------------------- 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: 0.9990 chunk 125 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 233 GLN B 233 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 = 0.3785 r_free = 0.3785 target = 0.150449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117661 restraints weight = 14461.716| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.15 r_work: 0.3322 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1678 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= 0.153 Angle : 0.523 5.468 17780 Z= 0.275 Chirality : 0.045 0.137 1955 Planarity : 0.004 0.042 2265 Dihedral : 4.363 18.608 1715 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.73 % Allowed : 10.97 % Favored : 87.29 % 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: 0.32 (0.22), residues: 1540 helix: 1.27 (0.23), residues: 530 sheet: 1.62 (0.27), residues: 435 loop : -2.04 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.007 0.001 TYR D 148 PHE 0.010 0.001 PHE D 116 TRP 0.024 0.001 TRP C 206 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00366 (13065) covalent geometry : angle 0.52305 (17780) hydrogen bonds : bond 0.03237 ( 600) hydrogen bonds : angle 4.39626 ( 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 189 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.515 Fit side-chains REVERT: A 36 ASP cc_start: 0.8911 (t0) cc_final: 0.8548 (t70) REVERT: A 69 ASN cc_start: 0.7520 (m-40) cc_final: 0.7308 (m-40) REVERT: A 150 GLU cc_start: 0.7847 (pm20) cc_final: 0.7442 (mp0) REVERT: A 155 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6803 (mm-30) REVERT: A 156 GLU cc_start: 0.7800 (tt0) cc_final: 0.7435 (tt0) REVERT: B 27 ASN cc_start: 0.7968 (t0) cc_final: 0.7546 (t0) REVERT: B 36 ASP cc_start: 0.9008 (t0) cc_final: 0.8778 (t70) REVERT: B 69 ASN cc_start: 0.7476 (m-40) cc_final: 0.7198 (m-40) REVERT: B 90 LYS cc_start: 0.8370 (pttt) cc_final: 0.7866 (ptpp) REVERT: B 93 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: B 150 GLU cc_start: 0.7813 (pm20) cc_final: 0.7208 (mp0) REVERT: B 155 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6794 (mm-30) REVERT: B 156 GLU cc_start: 0.7765 (tt0) cc_final: 0.7413 (tt0) REVERT: B 163 ARG cc_start: 0.7396 (mmt90) cc_final: 0.7123 (mmp80) REVERT: C 29 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7695 (tt) REVERT: C 34 LYS cc_start: 0.8454 (mttm) cc_final: 0.8148 (mttm) REVERT: C 90 LYS cc_start: 0.8234 (pttt) cc_final: 0.7687 (ptpp) REVERT: C 150 GLU cc_start: 0.7741 (pm20) cc_final: 0.7345 (mp0) REVERT: C 155 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6839 (mm-30) REVERT: C 159 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: D 34 LYS cc_start: 0.8356 (mttm) cc_final: 0.8128 (mttp) REVERT: D 90 LYS cc_start: 0.8349 (pttt) cc_final: 0.7791 (ptpp) REVERT: D 93 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8328 (mtp) REVERT: D 150 GLU cc_start: 0.7800 (pm20) cc_final: 0.7338 (mp0) REVERT: D 155 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6873 (mm-30) REVERT: D 163 ARG cc_start: 0.7418 (mmt90) cc_final: 0.7175 (mmp80) REVERT: D 176 ASP cc_start: 0.7981 (m-30) cc_final: 0.7646 (m-30) REVERT: E 93 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8349 (mtp) REVERT: E 150 GLU cc_start: 0.7893 (pm20) cc_final: 0.7427 (mp0) REVERT: E 155 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6937 (mm-30) REVERT: E 156 GLU cc_start: 0.7668 (tt0) cc_final: 0.7307 (tt0) REVERT: E 185 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7335 (pt0) outliers start: 24 outliers final: 14 residues processed: 173 average time/residue: 0.7137 time to fit residues: 132.3600 Evaluate side-chains 177 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain B residue 29 LEU 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 93 MET 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 Chi-restraints excluded: chain E residue 221 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 233 GLN B 233 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 = 0.3821 r_free = 0.3821 target = 0.152365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120805 restraints weight = 14268.958| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.08 r_work: 0.3345 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13065 Z= 0.123 Angle : 0.497 5.497 17780 Z= 0.260 Chirality : 0.045 0.140 1955 Planarity : 0.004 0.041 2265 Dihedral : 4.186 18.323 1715 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 12.06 % Favored : 85.92 % 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: 0.44 (0.22), residues: 1540 helix: 1.40 (0.23), residues: 530 sheet: 1.69 (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 C 163 TYR 0.006 0.001 TYR D 148 PHE 0.009 0.001 PHE D 116 TRP 0.023 0.001 TRP C 206 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00287 (13065) covalent geometry : angle 0.49681 (17780) hydrogen bonds : bond 0.02952 ( 600) hydrogen bonds : angle 4.26135 ( 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 186 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.586 Fit side-chains REVERT: A 69 ASN cc_start: 0.7516 (m-40) cc_final: 0.7303 (m-40) REVERT: A 150 GLU cc_start: 0.7809 (pm20) cc_final: 0.7462 (mp0) REVERT: A 155 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6880 (mm-30) REVERT: A 156 GLU cc_start: 0.7798 (tt0) cc_final: 0.7424 (tt0) REVERT: B 27 ASN cc_start: 0.7901 (t0) cc_final: 0.7463 (t0) REVERT: B 69 ASN cc_start: 0.7485 (m-40) cc_final: 0.7211 (m-40) REVERT: B 90 LYS cc_start: 0.8398 (pttt) cc_final: 0.7891 (ptpp) REVERT: B 93 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8240 (mtp) REVERT: B 155 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6736 (mm-30) REVERT: B 156 GLU cc_start: 0.7753 (tt0) cc_final: 0.7384 (tt0) REVERT: B 163 ARG cc_start: 0.7420 (mmt90) cc_final: 0.7144 (mmp80) REVERT: C 29 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7719 (tt) REVERT: C 34 LYS cc_start: 0.8458 (mttm) cc_final: 0.8134 (mttm) REVERT: C 36 ASP cc_start: 0.8896 (t0) cc_final: 0.8565 (t70) REVERT: C 90 LYS cc_start: 0.8211 (pttt) cc_final: 0.7640 (ptpp) REVERT: C 93 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: C 150 GLU cc_start: 0.7760 (pm20) cc_final: 0.7343 (mp0) REVERT: C 155 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6841 (mm-30) REVERT: D 27 ASN cc_start: 0.8085 (t0) cc_final: 0.7454 (t0) REVERT: D 34 LYS cc_start: 0.8324 (mttm) cc_final: 0.8072 (mmtp) REVERT: D 36 ASP cc_start: 0.8799 (t0) cc_final: 0.8391 (t70) REVERT: D 69 ASN cc_start: 0.7479 (m-40) cc_final: 0.7256 (m-40) REVERT: D 90 LYS cc_start: 0.8316 (pttt) cc_final: 0.7819 (ptpp) REVERT: D 93 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: D 150 GLU cc_start: 0.7817 (pm20) cc_final: 0.7331 (mp0) REVERT: D 155 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6836 (mm-30) REVERT: D 159 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6886 (pt0) REVERT: D 163 ARG cc_start: 0.7419 (mmt90) cc_final: 0.7217 (mmp80) REVERT: D 176 ASP cc_start: 0.7947 (m-30) cc_final: 0.7602 (m-30) REVERT: E 36 ASP cc_start: 0.8810 (t0) cc_final: 0.8556 (t70) REVERT: E 93 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: E 150 GLU cc_start: 0.7901 (pm20) cc_final: 0.7420 (mp0) REVERT: E 155 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6924 (mm-30) REVERT: E 156 GLU cc_start: 0.7732 (tt0) cc_final: 0.7309 (tt0) REVERT: E 185 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7377 (pt0) outliers start: 28 outliers final: 12 residues processed: 170 average time/residue: 0.6853 time to fit residues: 125.1854 Evaluate side-chains 171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain B residue 29 LEU 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 C residue 29 LEU Chi-restraints excluded: chain C residue 93 MET 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 221 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 184 ASN A 233 GLN C 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 = 0.3780 r_free = 0.3780 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117423 restraints weight = 14333.836| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.15 r_work: 0.3336 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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= 0.134 Angle : 0.504 5.391 17780 Z= 0.264 Chirality : 0.045 0.134 1955 Planarity : 0.004 0.041 2265 Dihedral : 4.155 18.363 1715 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.17 % Allowed : 12.56 % Favored : 85.27 % 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: 0.47 (0.22), residues: 1540 helix: 1.46 (0.23), residues: 530 sheet: 1.69 (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 C 163 TYR 0.007 0.001 TYR D 148 PHE 0.010 0.001 PHE A 116 TRP 0.025 0.001 TRP C 206 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00318 (13065) covalent geometry : angle 0.50363 (17780) hydrogen bonds : bond 0.02974 ( 600) hydrogen bonds : angle 4.25007 ( 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 181 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.471 Fit side-chains REVERT: A 36 ASP cc_start: 0.8885 (t0) cc_final: 0.8527 (t70) REVERT: A 69 ASN cc_start: 0.7493 (m-40) cc_final: 0.7281 (m-40) REVERT: A 150 GLU cc_start: 0.7810 (pm20) cc_final: 0.7449 (mp0) REVERT: A 155 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6869 (mm-30) REVERT: A 156 GLU cc_start: 0.7840 (tt0) cc_final: 0.7469 (tt0) REVERT: B 27 ASN cc_start: 0.7890 (t0) cc_final: 0.7413 (t0) REVERT: B 36 ASP cc_start: 0.8973 (t0) cc_final: 0.8575 (t70) REVERT: B 69 ASN cc_start: 0.7423 (m-40) cc_final: 0.7149 (m-40) REVERT: B 90 LYS cc_start: 0.8352 (pttt) cc_final: 0.7838 (ptpp) REVERT: B 93 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: B 155 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6711 (mm-30) REVERT: B 156 GLU cc_start: 0.7800 (tt0) cc_final: 0.7394 (tt0) REVERT: B 163 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7090 (mmp80) REVERT: C 29 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7674 (tt) REVERT: C 34 LYS cc_start: 0.8434 (mttm) cc_final: 0.8079 (mttm) REVERT: C 90 LYS cc_start: 0.8182 (pttt) cc_final: 0.7610 (ptpp) REVERT: C 93 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: C 137 ASN cc_start: 0.7484 (p0) cc_final: 0.7185 (p0) REVERT: C 150 GLU cc_start: 0.7747 (pm20) cc_final: 0.7302 (mp0) REVERT: C 155 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6757 (mm-30) REVERT: D 27 ASN cc_start: 0.8053 (t0) cc_final: 0.7379 (t0) REVERT: D 34 LYS cc_start: 0.8316 (mttm) cc_final: 0.8043 (mmtp) REVERT: D 69 ASN cc_start: 0.7450 (m-40) cc_final: 0.7227 (m-40) REVERT: D 90 LYS cc_start: 0.8263 (pttt) cc_final: 0.7749 (ptpp) REVERT: D 150 GLU cc_start: 0.7841 (pm20) cc_final: 0.7322 (mp0) REVERT: D 155 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6834 (mm-30) REVERT: D 159 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: E 93 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: E 150 GLU cc_start: 0.7872 (pm20) cc_final: 0.7410 (mp0) REVERT: E 155 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6925 (mm-30) REVERT: E 156 GLU cc_start: 0.7687 (tt0) cc_final: 0.7250 (tt0) REVERT: E 185 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7345 (pt0) outliers start: 30 outliers final: 22 residues processed: 165 average time/residue: 0.7309 time to fit residues: 129.4663 Evaluate side-chains 170 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 29 LEU 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 221 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU 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 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 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 221 SER 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: 6.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 0.0870 chunk 69 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 233 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120089 restraints weight = 14325.417| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.16 r_work: 0.3372 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1967 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= 0.096 Angle : 0.466 5.159 17780 Z= 0.243 Chirality : 0.044 0.138 1955 Planarity : 0.003 0.041 2265 Dihedral : 3.924 17.799 1715 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.02 % Allowed : 13.43 % 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: 0.64 (0.22), residues: 1540 helix: 1.60 (0.23), residues: 530 sheet: 1.83 (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 E 163 TYR 0.006 0.001 TYR B 203 PHE 0.008 0.001 PHE D 116 TRP 0.027 0.001 TRP E 206 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00216 (13065) covalent geometry : angle 0.46600 (17780) hydrogen bonds : bond 0.02572 ( 600) hydrogen bonds : angle 4.05314 ( 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 184 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.479 Fit side-chains REVERT: A 36 ASP cc_start: 0.8880 (t0) cc_final: 0.8509 (t70) REVERT: A 150 GLU cc_start: 0.7809 (pm20) cc_final: 0.7470 (mp0) REVERT: A 155 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6845 (mm-30) REVERT: A 156 GLU cc_start: 0.7798 (tt0) cc_final: 0.7387 (tt0) REVERT: A 163 ARG cc_start: 0.7201 (mmt90) cc_final: 0.6968 (mmt90) REVERT: B 27 ASN cc_start: 0.7848 (t0) cc_final: 0.7467 (t0) REVERT: B 69 ASN cc_start: 0.7365 (m-40) cc_final: 0.7084 (m-40) REVERT: B 90 LYS cc_start: 0.8296 (pttt) cc_final: 0.7806 (ptpp) REVERT: B 93 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: B 137 ASN cc_start: 0.7384 (p0) cc_final: 0.7175 (p0) REVERT: B 155 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6617 (mm-30) REVERT: B 156 GLU cc_start: 0.7779 (tt0) cc_final: 0.7345 (tt0) REVERT: B 163 ARG cc_start: 0.7323 (mmt90) cc_final: 0.7084 (mmp80) REVERT: C 27 ASN cc_start: 0.8039 (t0) cc_final: 0.7737 (t0) REVERT: C 29 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7478 (OUTLIER) REVERT: C 34 LYS cc_start: 0.8375 (mttm) cc_final: 0.8034 (mttm) REVERT: C 65 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.6011 (mtm110) REVERT: C 90 LYS cc_start: 0.8188 (pttt) cc_final: 0.7651 (ptpp) REVERT: C 93 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8274 (mtp) REVERT: C 137 ASN cc_start: 0.7300 (p0) cc_final: 0.7098 (p0) REVERT: C 150 GLU cc_start: 0.7706 (pm20) cc_final: 0.7260 (mp0) REVERT: C 155 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6722 (mm-30) REVERT: C 163 ARG cc_start: 0.7252 (mmt90) cc_final: 0.7010 (mmt90) REVERT: D 27 ASN cc_start: 0.7995 (t0) cc_final: 0.7417 (t0) REVERT: D 34 LYS cc_start: 0.8275 (mttm) cc_final: 0.8015 (mmtp) REVERT: D 36 ASP cc_start: 0.8777 (t0) cc_final: 0.8302 (t70) REVERT: D 86 ASP cc_start: 0.7692 (t70) cc_final: 0.7416 (t0) REVERT: D 90 LYS cc_start: 0.8229 (pttt) cc_final: 0.7692 (ptpp) REVERT: D 137 ASN cc_start: 0.7424 (p0) cc_final: 0.7125 (p0) REVERT: D 150 GLU cc_start: 0.7691 (pm20) cc_final: 0.7141 (mt-10) REVERT: D 155 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6842 (mm-30) REVERT: D 159 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: E 34 LYS cc_start: 0.8314 (mttm) cc_final: 0.8099 (mmtp) REVERT: E 93 MET cc_start: 0.8651 (ttp) cc_final: 0.8383 (mtp) REVERT: E 155 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6904 (mm-30) REVERT: E 163 ARG cc_start: 0.7350 (mmt90) cc_final: 0.7085 (mmt90) REVERT: E 185 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7346 (pt0) outliers start: 28 outliers final: 13 residues processed: 169 average time/residue: 0.7007 time to fit residues: 127.1991 Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 B residue 222 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 49 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 233 GLN D 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 = 0.3741 r_free = 0.3741 target = 0.145801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113749 restraints weight = 14331.142| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.10 r_work: 0.3288 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 13065 Z= 0.238 Angle : 0.582 6.894 17780 Z= 0.306 Chirality : 0.048 0.146 1955 Planarity : 0.004 0.039 2265 Dihedral : 4.476 21.157 1715 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.67 % Allowed : 13.72 % Favored : 83.61 % 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: 0.38 (0.22), residues: 1540 helix: 1.43 (0.23), residues: 530 sheet: 1.56 (0.28), residues: 435 loop : -2.05 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 91 TYR 0.009 0.002 TYR D 204 PHE 0.012 0.002 PHE C 116 TRP 0.027 0.002 TRP C 206 HIS 0.005 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00583 (13065) covalent geometry : angle 0.58209 (17780) hydrogen bonds : bond 0.03616 ( 600) hydrogen bonds : angle 4.47743 ( 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 178 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.489 Fit side-chains REVERT: A 36 ASP cc_start: 0.8930 (t0) cc_final: 0.8555 (t70) REVERT: A 69 ASN cc_start: 0.7685 (m-40) cc_final: 0.7453 (m-40) REVERT: A 155 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6939 (mm-30) REVERT: B 36 ASP cc_start: 0.9019 (t0) cc_final: 0.8747 (t70) REVERT: B 90 LYS cc_start: 0.8423 (pttt) cc_final: 0.7921 (ptpp) REVERT: B 155 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6765 (mm-30) REVERT: B 156 GLU cc_start: 0.7789 (tt0) cc_final: 0.7471 (tt0) REVERT: C 27 ASN cc_start: 0.8358 (t0) cc_final: 0.7884 (t0) REVERT: C 34 LYS cc_start: 0.8520 (mttm) cc_final: 0.8136 (mttm) REVERT: C 36 ASP cc_start: 0.8955 (t0) cc_final: 0.8578 (t70) REVERT: C 90 LYS cc_start: 0.8309 (pttt) cc_final: 0.7751 (ptpp) REVERT: C 99 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7403 (ptm-80) REVERT: C 150 GLU cc_start: 0.7956 (pm20) cc_final: 0.7404 (mp0) REVERT: C 155 GLU cc_start: 0.7566 (mt-10) cc_final: 0.6788 (mm-30) REVERT: D 34 LYS cc_start: 0.8362 (mttm) cc_final: 0.8128 (mmtp) REVERT: D 36 ASP cc_start: 0.8863 (t0) cc_final: 0.8522 (t70) REVERT: D 69 ASN cc_start: 0.7652 (m-40) cc_final: 0.7400 (m-40) REVERT: D 86 ASP cc_start: 0.7793 (t70) cc_final: 0.7523 (t0) REVERT: D 90 LYS cc_start: 0.8392 (pttt) cc_final: 0.7800 (ptpp) REVERT: D 150 GLU cc_start: 0.7886 (pm20) cc_final: 0.7361 (mt-10) REVERT: D 155 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6881 (mm-30) REVERT: E 36 ASP cc_start: 0.8863 (t0) cc_final: 0.8539 (t70) REVERT: E 150 GLU cc_start: 0.7952 (pm20) cc_final: 0.7511 (mp0) REVERT: E 155 GLU cc_start: 0.7762 (mt-10) cc_final: 0.6999 (mm-30) REVERT: E 156 GLU cc_start: 0.7779 (tt0) cc_final: 0.7481 (tt0) REVERT: E 185 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7446 (pt0) outliers start: 37 outliers final: 17 residues processed: 164 average time/residue: 0.6766 time to fit residues: 119.5227 Evaluate side-chains 153 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 99 ARG 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 181 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 233 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115536 restraints weight = 14379.393| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.13 r_work: 0.3314 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13065 Z= 0.162 Angle : 0.532 5.552 17780 Z= 0.279 Chirality : 0.046 0.132 1955 Planarity : 0.004 0.040 2265 Dihedral : 4.328 19.365 1715 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.02 % Allowed : 14.80 % Favored : 83.18 % 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: 0.41 (0.22), residues: 1540 helix: 1.48 (0.23), residues: 530 sheet: 1.59 (0.28), residues: 435 loop : -2.06 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 163 TYR 0.007 0.001 TYR E 148 PHE 0.011 0.001 PHE D 116 TRP 0.030 0.002 TRP C 206 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00390 (13065) covalent geometry : angle 0.53181 (17780) hydrogen bonds : bond 0.03168 ( 600) hydrogen bonds : angle 4.36666 ( 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 162 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.465 Fit side-chains REVERT: A 36 ASP cc_start: 0.8866 (t0) cc_final: 0.8515 (t70) REVERT: A 69 ASN cc_start: 0.7633 (m-40) cc_final: 0.7398 (m-40) REVERT: A 99 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6249 (ptm160) REVERT: A 155 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6855 (mm-30) REVERT: A 304 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: B 27 ASN cc_start: 0.8250 (t0) cc_final: 0.7892 (t0) REVERT: B 36 ASP cc_start: 0.8990 (t0) cc_final: 0.8605 (t70) REVERT: B 90 LYS cc_start: 0.8369 (pttt) cc_final: 0.7842 (ptpp) REVERT: B 93 MET cc_start: 0.8618 (ttm) cc_final: 0.8207 (mtp) REVERT: B 145 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7859 (tt) REVERT: B 155 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6708 (mm-30) REVERT: B 156 GLU cc_start: 0.7706 (tt0) cc_final: 0.7342 (tt0) REVERT: C 27 ASN cc_start: 0.8258 (t0) cc_final: 0.7809 (t0) REVERT: C 34 LYS cc_start: 0.8428 (mttm) cc_final: 0.8075 (mttm) REVERT: C 36 ASP cc_start: 0.8909 (t0) cc_final: 0.8519 (t70) REVERT: C 90 LYS cc_start: 0.8212 (pttt) cc_final: 0.7634 (ptpp) REVERT: C 150 GLU cc_start: 0.7788 (pm20) cc_final: 0.7255 (mp0) REVERT: C 155 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6736 (mm-30) REVERT: D 34 LYS cc_start: 0.8310 (mttm) cc_final: 0.8042 (mmtp) REVERT: D 69 ASN cc_start: 0.7519 (m-40) cc_final: 0.7268 (m-40) REVERT: D 86 ASP cc_start: 0.7669 (t70) cc_final: 0.7392 (t0) REVERT: D 90 LYS cc_start: 0.8290 (pttt) cc_final: 0.7680 (ptpp) REVERT: D 137 ASN cc_start: 0.7677 (p0) cc_final: 0.7401 (p0) REVERT: D 155 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6935 (mm-30) REVERT: E 36 ASP cc_start: 0.8826 (t0) cc_final: 0.8489 (t70) REVERT: E 93 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8424 (mtp) REVERT: E 155 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6914 (mm-30) REVERT: E 156 GLU cc_start: 0.7734 (tt0) cc_final: 0.7398 (tt0) REVERT: E 185 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7372 (pt0) outliers start: 28 outliers final: 21 residues processed: 153 average time/residue: 0.6617 time to fit residues: 109.0194 Evaluate side-chains 159 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 145 ILE 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 B residue 304 PHE Chi-restraints excluded: chain C residue 29 LEU 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 C residue 304 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 222 VAL 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 136 ASN 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 67 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 233 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117637 restraints weight = 14400.663| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.16 r_work: 0.3329 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13065 Z= 0.116 Angle : 0.494 5.663 17780 Z= 0.258 Chirality : 0.044 0.133 1955 Planarity : 0.004 0.041 2265 Dihedral : 4.105 18.449 1715 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 15.02 % Favored : 82.96 % 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: 1.61 (0.23), residues: 530 sheet: 1.68 (0.27), residues: 435 loop : -2.04 (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 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00269 (13065) covalent geometry : angle 0.49443 (17780) hydrogen bonds : bond 0.02786 ( 600) hydrogen bonds : angle 4.18810 ( 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 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.483 Fit side-chains REVERT: A 36 ASP cc_start: 0.8866 (t0) cc_final: 0.8528 (t70) REVERT: A 69 ASN cc_start: 0.7458 (m-40) cc_final: 0.7237 (m-40) REVERT: A 150 GLU cc_start: 0.7837 (pm20) cc_final: 0.7408 (mp0) REVERT: A 155 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6851 (mm-30) REVERT: A 156 GLU cc_start: 0.7743 (tt0) cc_final: 0.7357 (tt0) REVERT: A 304 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: B 69 ASN cc_start: 0.7458 (m-40) cc_final: 0.7198 (m-40) REVERT: B 90 LYS cc_start: 0.8360 (pttt) cc_final: 0.7851 (ptpp) REVERT: B 93 MET cc_start: 0.8599 (ttm) cc_final: 0.8182 (mtp) REVERT: B 137 ASN cc_start: 0.7502 (p0) cc_final: 0.7209 (p0) REVERT: B 145 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 150 GLU cc_start: 0.7789 (pm20) cc_final: 0.7187 (mp0) REVERT: B 155 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6675 (mm-30) REVERT: B 156 GLU cc_start: 0.7661 (tt0) cc_final: 0.7271 (tt0) REVERT: B 174 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7582 (ttm-80) REVERT: C 27 ASN cc_start: 0.8141 (t0) cc_final: 0.7735 (t0) REVERT: C 34 LYS cc_start: 0.8415 (mttm) cc_final: 0.8057 (mttm) REVERT: C 90 LYS cc_start: 0.8186 (pttt) cc_final: 0.7582 (ptpp) REVERT: C 93 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8313 (mtp) REVERT: C 137 ASN cc_start: 0.7489 (p0) cc_final: 0.7196 (p0) REVERT: C 150 GLU cc_start: 0.7722 (pm20) cc_final: 0.7218 (mp0) REVERT: C 155 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6729 (mm-30) REVERT: C 304 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: D 34 LYS cc_start: 0.8283 (mttm) cc_final: 0.7999 (mmtp) REVERT: D 69 ASN cc_start: 0.7434 (m-40) cc_final: 0.7196 (m-40) REVERT: D 86 ASP cc_start: 0.7654 (t70) cc_final: 0.7377 (t0) REVERT: D 90 LYS cc_start: 0.8300 (pttt) cc_final: 0.7772 (ptpp) REVERT: D 137 ASN cc_start: 0.7532 (p0) cc_final: 0.7221 (p0) REVERT: D 150 GLU cc_start: 0.7743 (pm20) cc_final: 0.7183 (mt-10) REVERT: D 155 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6852 (mm-30) REVERT: D 156 GLU cc_start: 0.7666 (tt0) cc_final: 0.7145 (tp30) REVERT: E 36 ASP cc_start: 0.8815 (t0) cc_final: 0.8567 (t70) REVERT: E 155 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6839 (mm-30) REVERT: E 156 GLU cc_start: 0.7709 (tt0) cc_final: 0.7381 (tt0) REVERT: E 163 ARG cc_start: 0.7098 (mmt90) cc_final: 0.6866 (mmp80) REVERT: E 185 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7423 (pt0) outliers start: 28 outliers final: 19 residues processed: 163 average time/residue: 0.6089 time to fit residues: 107.3671 Evaluate side-chains 166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 181 VAL 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 C residue 304 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN 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: 1.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.0470 chunk 106 optimal weight: 0.2980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 233 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120201 restraints weight = 14311.416| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.16 r_work: 0.3366 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13065 Z= 0.096 Angle : 0.470 5.567 17780 Z= 0.244 Chirality : 0.044 0.137 1955 Planarity : 0.004 0.047 2265 Dihedral : 3.889 17.930 1715 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.81 % Allowed : 15.23 % Favored : 82.96 % 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: 0.66 (0.23), residues: 1540 helix: 1.71 (0.23), residues: 530 sheet: 1.77 (0.27), residues: 435 loop : -2.01 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 163 TYR 0.006 0.001 TYR B 203 PHE 0.008 0.001 PHE D 116 TRP 0.036 0.001 TRP C 206 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00216 (13065) covalent geometry : angle 0.46958 (17780) hydrogen bonds : bond 0.02534 ( 600) hydrogen bonds : angle 4.02178 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.35 seconds wall clock time: 69 minutes 2.26 seconds (4142.26 seconds total)