Starting phenix.real_space_refine on Thu Feb 5 08:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mbx_63781/02_2026/9mbx_63781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mbx_63781/02_2026/9mbx_63781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mbx_63781/02_2026/9mbx_63781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mbx_63781/02_2026/9mbx_63781.map" model { file = "/net/cci-nas-00/data/ceres_data/9mbx_63781/02_2026/9mbx_63781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mbx_63781/02_2026/9mbx_63781.cif" } resolution = 3.8 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= 0.013 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 10045 2.51 5 N 2737 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 15981 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "B" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2283 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Time building chain proxies: 3.62, per 1000 atoms: 0.23 Number of scatterers: 15981 At special positions: 0 Unit cell: (109.48, 110.4, 93.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 3150 8.00 N 2737 7.00 C 10045 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: 1.24 Conformation dependent library (CDL) restraints added in 762.5 milliseconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 55 sheets defined 5.6% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.886A pdb=" N VAL F 140 " --> pdb=" O GLY F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 removed outlier: 3.834A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.894A pdb=" N VAL A 140 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.826A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.868A pdb=" N VAL B 140 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.837A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.861A pdb=" N VAL C 140 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.839A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.866A pdb=" N VAL D 140 " --> pdb=" O GLY D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.841A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.866A pdb=" N VAL E 140 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 removed outlier: 3.849A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 136 through 140 removed outlier: 3.883A pdb=" N VAL G 140 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 222 removed outlier: 3.843A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 21 through 22 removed outlier: 3.508A pdb=" N MET F 234 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 232 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE F 228 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'F' and resid 66 through 70 removed outlier: 5.897A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG F 251 " --> pdb=" O TRP F 274 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP F 274 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG F 253 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP F 272 " --> pdb=" O ARG F 253 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP F 255 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 83 through 88 removed outlier: 4.164A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 149 through 151 removed outlier: 3.670A pdb=" N LYS G 110 " --> pdb=" O GLN F 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'F' and resid 187 through 188 Processing sheet with id=AA8, first strand: chain 'F' and resid 242 through 247 removed outlier: 3.897A pdb=" N THR F 243 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 284 " --> pdb=" O THR F 243 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS F 283 " --> pdb=" O THR F 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.567A pdb=" N ILE A 232 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 228 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 70 removed outlier: 5.918A pdb=" N VAL A 67 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 79 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 69 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG A 251 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP A 274 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 253 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP A 272 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A 255 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 83 through 88 removed outlier: 4.117A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AB5, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AB6, first strand: chain 'A' and resid 242 through 247 removed outlier: 3.900A pdb=" N THR A 243 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 284 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 283 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.569A pdb=" N ILE B 232 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 228 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AB9, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AC1, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.883A pdb=" N VAL B 67 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 79 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER B 69 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 88 removed outlier: 4.120A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.779A pdb=" N LYS B 110 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 150 " --> pdb=" O LYS B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AC5, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AC6, first strand: chain 'B' and resid 242 through 247 removed outlier: 3.868A pdb=" N THR B 243 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 284 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 283 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 21 through 22 removed outlier: 3.574A pdb=" N ILE C 232 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 228 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AC9, first strand: chain 'C' and resid 66 through 70 removed outlier: 5.899A pdb=" N VAL C 67 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA C 79 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C 69 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG C 251 " --> pdb=" O TRP C 274 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP C 274 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG C 253 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP C 272 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 255 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 88 removed outlier: 4.178A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.680A pdb=" N LYS C 110 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AD4, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AD5, first strand: chain 'C' and resid 242 through 247 removed outlier: 3.870A pdb=" N THR C 243 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 284 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS C 283 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.569A pdb=" N ILE D 232 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 228 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA D 229 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR D 101 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL D 231 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AD8, first strand: chain 'D' and resid 66 through 70 removed outlier: 5.926A pdb=" N VAL D 67 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA D 79 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER D 69 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 83 through 88 removed outlier: 4.148A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 109 through 110 removed outlier: 3.716A pdb=" N LYS D 110 " --> pdb=" O GLN E 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 173 through 175 Processing sheet with id=AE3, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AE4, first strand: chain 'D' and resid 242 through 247 removed outlier: 3.896A pdb=" N THR D 243 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 284 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS D 283 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 21 through 22 removed outlier: 3.575A pdb=" N ILE E 232 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 228 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA E 229 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR E 101 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AE7, first strand: chain 'E' and resid 66 through 70 removed outlier: 5.914A pdb=" N VAL E 67 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA E 79 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER E 69 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 83 through 88 removed outlier: 4.074A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 109 through 110 removed outlier: 3.633A pdb=" N LYS E 110 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 173 through 175 Processing sheet with id=AF2, first strand: chain 'E' and resid 187 through 188 Processing sheet with id=AF3, first strand: chain 'E' and resid 242 through 247 removed outlier: 3.907A pdb=" N THR E 243 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 284 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS E 283 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.598A pdb=" N ILE G 232 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE G 228 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA G 229 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR G 101 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 26 through 28 Processing sheet with id=AF6, first strand: chain 'G' and resid 66 through 70 removed outlier: 5.906A pdb=" N VAL G 67 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA G 79 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER G 69 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 83 through 88 removed outlier: 4.109A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AF9, first strand: chain 'G' and resid 187 through 188 Processing sheet with id=AG1, first strand: chain 'G' and resid 242 through 247 removed outlier: 3.883A pdb=" N THR G 243 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 284 " --> pdb=" O THR G 243 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS G 283 " --> pdb=" O THR G 292 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1002 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: 2.56 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5201 1.34 - 1.46: 3691 1.46 - 1.58: 7348 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 16338 Sorted by residual: bond pdb=" CA VAL G 86 " pdb=" CB VAL G 86 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.08e-02 8.57e+03 8.25e-01 bond pdb=" CA VAL G 67 " pdb=" CB VAL G 67 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 8.00e-01 bond pdb=" CA VAL B 67 " pdb=" CB VAL B 67 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.89e-01 bond pdb=" CA VAL D 67 " pdb=" CB VAL D 67 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.53e-01 bond pdb=" CA VAL F 67 " pdb=" CB VAL F 67 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.41e-01 ... (remaining 16333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 21273 1.49 - 2.97: 718 2.97 - 4.46: 87 4.46 - 5.95: 23 5.95 - 7.43: 5 Bond angle restraints: 22106 Sorted by residual: angle pdb=" N ALA B 83 " pdb=" CA ALA B 83 " pdb=" C ALA B 83 " ideal model delta sigma weight residual 107.23 111.65 -4.42 1.67e+00 3.59e-01 7.01e+00 angle pdb=" N ALA E 83 " pdb=" CA ALA E 83 " pdb=" C ALA E 83 " ideal model delta sigma weight residual 107.23 111.65 -4.42 1.67e+00 3.59e-01 7.00e+00 angle pdb=" N ALA D 83 " pdb=" CA ALA D 83 " pdb=" C ALA D 83 " ideal model delta sigma weight residual 107.23 111.62 -4.39 1.67e+00 3.59e-01 6.91e+00 angle pdb=" N ALA F 83 " pdb=" CA ALA F 83 " pdb=" C ALA F 83 " ideal model delta sigma weight residual 107.23 111.59 -4.36 1.67e+00 3.59e-01 6.82e+00 angle pdb=" N ALA G 83 " pdb=" CA ALA G 83 " pdb=" C ALA G 83 " ideal model delta sigma weight residual 107.23 111.57 -4.34 1.67e+00 3.59e-01 6.77e+00 ... (remaining 22101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.11: 8575 11.11 - 22.22: 732 22.22 - 33.33: 283 33.33 - 44.44: 81 44.44 - 55.54: 38 Dihedral angle restraints: 9709 sinusoidal: 3941 harmonic: 5768 Sorted by residual: dihedral pdb=" CA LEU A 88 " pdb=" CB LEU A 88 " pdb=" CG LEU A 88 " pdb=" CD1 LEU A 88 " ideal model delta sinusoidal sigma weight residual 60.00 115.54 -55.54 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" N MET G 113 " pdb=" CA MET G 113 " pdb=" CB MET G 113 " pdb=" CG MET G 113 " ideal model delta sinusoidal sigma weight residual -60.00 -112.54 52.54 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" N LYS B 271 " pdb=" CA LYS B 271 " pdb=" CB LYS B 271 " pdb=" CG LYS B 271 " ideal model delta sinusoidal sigma weight residual -60.00 -109.57 49.57 3 1.50e+01 4.44e-03 8.79e+00 ... (remaining 9706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1408 0.028 - 0.055: 641 0.055 - 0.083: 130 0.083 - 0.110: 130 0.110 - 0.138: 43 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CA ILE E 61 " pdb=" N ILE E 61 " pdb=" C ILE E 61 " pdb=" CB ILE E 61 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE D 61 " pdb=" N ILE D 61 " pdb=" C ILE D 61 " pdb=" CB ILE D 61 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE C 61 " pdb=" N ILE C 61 " pdb=" C ILE C 61 " pdb=" CB ILE C 61 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2349 not shown) Planarity restraints: 2849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 90 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO G 91 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 90 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO C 91 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 90 " -0.018 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO F 91 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 91 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 91 " -0.016 5.00e-02 4.00e+02 ... (remaining 2846 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1344 2.74 - 3.28: 16428 3.28 - 3.82: 26718 3.82 - 4.36: 32417 4.36 - 4.90: 54802 Nonbonded interactions: 131709 Sorted by model distance: nonbonded pdb=" OD1 ASN F 105 " pdb=" OG SER A 218 " model vdw 2.201 3.040 nonbonded pdb=" OG SER F 218 " pdb=" OD1 ASN G 105 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN A 105 " pdb=" OG SER B 218 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASN E 105 " pdb=" OG SER G 218 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN B 105 " pdb=" OG SER C 218 " model vdw 2.216 3.040 ... (remaining 131704 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: 0.03 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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 group one per residue 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: 1.450 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.470 Find NCS groups from input model: 0.110 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 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 : 0.002 0.022 16338 Z= 0.138 Angle : 0.634 7.433 22106 Z= 0.381 Chirality : 0.040 0.138 2352 Planarity : 0.002 0.029 2849 Dihedral : 10.891 55.544 6013 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.63 % Allowed : 10.54 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.70 (0.19), residues: 1960 helix: None (None), residues: 0 sheet: -1.76 (0.18), residues: 840 loop : -1.79 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.007 0.001 TYR B 68 PHE 0.009 0.001 PHE F 39 TRP 0.007 0.001 TRP E 167 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00225 (16338) covalent geometry : angle 0.63435 (22106) hydrogen bonds : bond 0.31632 ( 408) hydrogen bonds : angle 14.05518 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 467 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 171 PHE cc_start: 0.7237 (t80) cc_final: 0.6542 (t80) REVERT: F 174 MET cc_start: 0.5548 (mmm) cc_final: 0.5258 (mmm) REVERT: A 171 PHE cc_start: 0.7215 (t80) cc_final: 0.6200 (t80) REVERT: A 174 MET cc_start: 0.5774 (mmm) cc_final: 0.5413 (mmm) REVERT: A 286 TRP cc_start: 0.6809 (m100) cc_final: 0.6450 (m100) REVERT: B 6 ASN cc_start: 0.6894 (m110) cc_final: 0.6385 (t0) REVERT: B 171 PHE cc_start: 0.7240 (t80) cc_final: 0.6588 (t80) REVERT: C 136 ILE cc_start: 0.7188 (pt) cc_final: 0.6968 (mp) REVERT: C 171 PHE cc_start: 0.7078 (t80) cc_final: 0.6193 (t80) REVERT: D 171 PHE cc_start: 0.7329 (t80) cc_final: 0.6274 (t80) REVERT: D 174 MET cc_start: 0.5245 (mmm) cc_final: 0.5040 (mmm) REVERT: D 286 TRP cc_start: 0.6876 (m100) cc_final: 0.6508 (m100) REVERT: E 171 PHE cc_start: 0.7178 (t80) cc_final: 0.6457 (t80) REVERT: E 174 MET cc_start: 0.5592 (mmm) cc_final: 0.5387 (mmm) REVERT: G 6 ASN cc_start: 0.6924 (m110) cc_final: 0.6470 (t0) REVERT: G 171 PHE cc_start: 0.7138 (t80) cc_final: 0.6592 (t80) REVERT: G 173 ASN cc_start: 0.7342 (p0) cc_final: 0.7003 (p0) REVERT: G 174 MET cc_start: 0.5552 (mmm) cc_final: 0.5223 (mmm) outliers start: 64 outliers final: 18 residues processed: 525 average time/residue: 0.1392 time to fit residues: 106.1199 Evaluate side-chains 303 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 165 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN F 176 ASN F 188 ASN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN F 269 ASN A 93 ASN A 150 GLN A 176 ASN A 188 ASN A 257 GLN A 269 ASN A 293 ASN B 93 ASN B 150 GLN B 176 ASN B 188 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 269 ASN C 6 ASN C 32 ASN C 93 ASN C 150 GLN C 173 ASN C 176 ASN C 188 ASN C 269 ASN D 93 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 269 ASN D 293 ASN E 93 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN E 188 ASN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN E 269 ASN E 293 ASN ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN G 188 ASN G 257 GLN G 269 ASN G 293 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.184278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.150710 restraints weight = 26282.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.154094 restraints weight = 17442.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.156158 restraints weight = 13543.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.157432 restraints weight = 11624.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.158264 restraints weight = 10582.589| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16338 Z= 0.194 Angle : 0.710 11.182 22106 Z= 0.370 Chirality : 0.045 0.154 2352 Planarity : 0.004 0.032 2849 Dihedral : 6.098 49.951 2179 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.38 % Allowed : 18.42 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.75 (0.18), residues: 1960 helix: None (None), residues: 0 sheet: -1.47 (0.18), residues: 833 loop : -2.13 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 253 TYR 0.014 0.002 TYR C 118 PHE 0.014 0.002 PHE C 42 TRP 0.027 0.002 TRP B 80 HIS 0.002 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00440 (16338) covalent geometry : angle 0.70959 (22106) hydrogen bonds : bond 0.05055 ( 408) hydrogen bonds : angle 9.14161 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 311 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 ASN cc_start: 0.6796 (m-40) cc_final: 0.6319 (t0) REVERT: F 112 TYR cc_start: 0.6779 (t80) cc_final: 0.6389 (t80) REVERT: F 196 PHE cc_start: 0.7074 (m-10) cc_final: 0.6596 (m-10) REVERT: F 234 MET cc_start: 0.6028 (mtp) cc_final: 0.5749 (mtm) REVERT: A 150 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6868 (pm20) REVERT: A 196 PHE cc_start: 0.7116 (m-10) cc_final: 0.6875 (m-10) REVERT: A 286 TRP cc_start: 0.6897 (m100) cc_final: 0.6428 (m100) REVERT: B 196 PHE cc_start: 0.6827 (m-10) cc_final: 0.6564 (m-10) REVERT: C 174 MET cc_start: 0.7201 (mmm) cc_final: 0.6972 (mmm) REVERT: C 260 TRP cc_start: 0.6633 (t60) cc_final: 0.6392 (t60) REVERT: D 194 GLN cc_start: 0.7458 (mm110) cc_final: 0.7147 (mm110) REVERT: E 196 PHE cc_start: 0.6999 (m-10) cc_final: 0.6392 (m-10) REVERT: G 171 PHE cc_start: 0.7888 (t80) cc_final: 0.7301 (t80) REVERT: G 194 GLN cc_start: 0.7987 (mt0) cc_final: 0.7705 (mm110) outliers start: 42 outliers final: 36 residues processed: 344 average time/residue: 0.1327 time to fit residues: 67.5289 Evaluate side-chains 286 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 ASN Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 293 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 165 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN F 293 ASN A 32 ASN A 150 GLN A 264 ASN A 293 ASN B 173 ASN B 176 ASN B 293 ASN C 6 ASN C 123 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN D 6 ASN D 150 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 293 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.182826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.148557 restraints weight = 26783.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.151883 restraints weight = 17618.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.154056 restraints weight = 13686.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.155347 restraints weight = 11744.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.156188 restraints weight = 10710.270| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16338 Z= 0.180 Angle : 0.667 10.607 22106 Z= 0.345 Chirality : 0.044 0.153 2352 Planarity : 0.004 0.033 2849 Dihedral : 6.164 49.647 2173 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.93 % Allowed : 19.61 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.88 (0.18), residues: 1960 helix: None (None), residues: 0 sheet: -1.78 (0.17), residues: 917 loop : -1.99 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 253 TYR 0.015 0.002 TYR B 65 PHE 0.024 0.002 PHE C 171 TRP 0.032 0.002 TRP D 80 HIS 0.002 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00407 (16338) covalent geometry : angle 0.66711 (22106) hydrogen bonds : bond 0.03975 ( 408) hydrogen bonds : angle 8.35732 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 273 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 ASN cc_start: 0.6958 (m-40) cc_final: 0.6354 (t0) REVERT: F 92 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7115 (p0) REVERT: F 174 MET cc_start: 0.4911 (mmm) cc_final: 0.4653 (mmm) REVERT: F 209 ASN cc_start: 0.5545 (t0) cc_final: 0.5319 (t0) REVERT: A 110 LYS cc_start: 0.7327 (mtmt) cc_final: 0.7017 (mtmt) REVERT: A 150 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: A 196 PHE cc_start: 0.7059 (m-10) cc_final: 0.6785 (m-10) REVERT: A 286 TRP cc_start: 0.7191 (m100) cc_final: 0.6489 (m100) REVERT: B 50 LYS cc_start: 0.6716 (mmmt) cc_final: 0.6231 (mttt) REVERT: B 174 MET cc_start: 0.6679 (mmm) cc_final: 0.5543 (mmm) REVERT: C 78 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8082 (tt) REVERT: C 174 MET cc_start: 0.7140 (mmm) cc_final: 0.6770 (mmm) REVERT: C 196 PHE cc_start: 0.6981 (m-10) cc_final: 0.6715 (m-10) REVERT: C 209 ASN cc_start: 0.5610 (t0) cc_final: 0.5303 (t0) REVERT: D 78 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (tt) REVERT: D 92 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7304 (p0) REVERT: D 171 PHE cc_start: 0.7806 (t80) cc_final: 0.7426 (t80) REVERT: D 174 MET cc_start: 0.4479 (mmm) cc_final: 0.4053 (mmm) REVERT: D 194 GLN cc_start: 0.7458 (mm110) cc_final: 0.7091 (mm110) REVERT: E 171 PHE cc_start: 0.7846 (t80) cc_final: 0.7029 (t80) REVERT: E 174 MET cc_start: 0.4954 (mmm) cc_final: 0.4412 (mmm) REVERT: E 196 PHE cc_start: 0.6892 (m-10) cc_final: 0.6411 (m-10) REVERT: E 248 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7500 (mp) REVERT: G 171 PHE cc_start: 0.7710 (t80) cc_final: 0.7504 (t80) outliers start: 87 outliers final: 57 residues processed: 343 average time/residue: 0.1235 time to fit residues: 64.3597 Evaluate side-chains 302 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 165 optimal weight: 0.0770 chunk 75 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 244 ASN F 293 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN B 244 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 244 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.181812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.145625 restraints weight = 26907.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.148109 restraints weight = 20096.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.149711 restraints weight = 16836.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.150734 restraints weight = 15116.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.151385 restraints weight = 14128.768| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 16338 Z= 0.358 Angle : 0.871 11.540 22106 Z= 0.456 Chirality : 0.050 0.175 2352 Planarity : 0.005 0.035 2849 Dihedral : 7.167 50.437 2173 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 6.52 % Allowed : 18.76 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -3.47 (0.18), residues: 1960 helix: None (None), residues: 0 sheet: -2.29 (0.17), residues: 854 loop : -2.31 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 253 TYR 0.029 0.003 TYR B 65 PHE 0.025 0.004 PHE C 42 TRP 0.037 0.003 TRP D 80 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00819 (16338) covalent geometry : angle 0.87054 (22106) hydrogen bonds : bond 0.05092 ( 408) hydrogen bonds : angle 8.85313 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 217 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 113 MET cc_start: 0.6060 (tpt) cc_final: 0.5656 (tpt) REVERT: F 168 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7822 (ptpp) REVERT: F 174 MET cc_start: 0.4997 (mmm) cc_final: 0.4738 (mmm) REVERT: F 204 MET cc_start: 0.7637 (pmm) cc_final: 0.7436 (pmm) REVERT: F 248 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7474 (mp) REVERT: F 251 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8255 (ttp80) REVERT: A 147 LYS cc_start: 0.7809 (tppt) cc_final: 0.7303 (ttpp) REVERT: A 150 GLN cc_start: 0.7433 (pm20) cc_final: 0.7125 (pm20) REVERT: A 168 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7877 (mttp) REVERT: A 174 MET cc_start: 0.5289 (mmm) cc_final: 0.4955 (mmm) REVERT: A 224 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 92 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7924 (p0) REVERT: B 158 GLU cc_start: 0.4669 (OUTLIER) cc_final: 0.4275 (tp30) REVERT: B 286 TRP cc_start: 0.7381 (m100) cc_final: 0.6920 (m100) REVERT: C 50 LYS cc_start: 0.6644 (mmmt) cc_final: 0.6358 (mtpt) REVERT: C 78 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8223 (tt) REVERT: C 168 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7510 (mttp) REVERT: C 174 MET cc_start: 0.6954 (mmm) cc_final: 0.6223 (mmm) REVERT: C 234 MET cc_start: 0.6619 (mtp) cc_final: 0.6298 (mtp) REVERT: C 235 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7212 (t0) REVERT: D 78 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8283 (tt) REVERT: D 158 GLU cc_start: 0.4747 (OUTLIER) cc_final: 0.4444 (tp30) REVERT: E 158 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.4352 (tp30) REVERT: E 174 MET cc_start: 0.5128 (mmm) cc_final: 0.4900 (mmm) REVERT: E 248 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (mp) REVERT: G 158 GLU cc_start: 0.4798 (OUTLIER) cc_final: 0.4432 (tp30) REVERT: G 174 MET cc_start: 0.6043 (mmm) cc_final: 0.5826 (mmm) outliers start: 115 outliers final: 76 residues processed: 318 average time/residue: 0.1190 time to fit residues: 57.6156 Evaluate side-chains 292 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 201 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 224 PHE Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 ASN F 293 ASN A 150 GLN A 173 ASN B 173 ASN C 173 ASN C 244 ASN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.182520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.148781 restraints weight = 26417.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.152068 restraints weight = 17549.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.154155 restraints weight = 13678.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.155514 restraints weight = 11790.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.156203 restraints weight = 10746.073| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16338 Z= 0.135 Angle : 0.643 11.011 22106 Z= 0.331 Chirality : 0.044 0.155 2352 Planarity : 0.003 0.036 2849 Dihedral : 6.278 48.853 2173 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.78 % Allowed : 19.84 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.91 (0.18), residues: 1960 helix: None (None), residues: 0 sheet: -1.78 (0.17), residues: 840 loop : -2.06 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.012 0.001 TYR G 102 PHE 0.020 0.002 PHE C 196 TRP 0.032 0.002 TRP F 260 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00292 (16338) covalent geometry : angle 0.64280 (22106) hydrogen bonds : bond 0.03386 ( 408) hydrogen bonds : angle 7.75736 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 256 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 150 GLN cc_start: 0.6968 (pm20) cc_final: 0.6697 (pm20) REVERT: F 174 MET cc_start: 0.4584 (mmm) cc_final: 0.4366 (mmm) REVERT: F 205 LYS cc_start: 0.7593 (tppt) cc_final: 0.6121 (ttmm) REVERT: A 147 LYS cc_start: 0.7779 (tppt) cc_final: 0.7045 (ttmm) REVERT: A 150 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6801 (pm20) REVERT: A 174 MET cc_start: 0.4962 (mmm) cc_final: 0.4700 (mmm) REVERT: B 25 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7006 (tt) REVERT: B 92 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 158 GLU cc_start: 0.3778 (OUTLIER) cc_final: 0.3543 (tp30) REVERT: B 171 PHE cc_start: 0.7815 (t80) cc_final: 0.7599 (t80) REVERT: B 174 MET cc_start: 0.4326 (mmm) cc_final: 0.3924 (mmm) REVERT: B 286 TRP cc_start: 0.7343 (m100) cc_final: 0.6988 (m100) REVERT: C 174 MET cc_start: 0.7136 (mmm) cc_final: 0.6141 (mmm) REVERT: D 78 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8133 (tt) REVERT: D 158 GLU cc_start: 0.4088 (OUTLIER) cc_final: 0.3872 (tp30) REVERT: D 171 PHE cc_start: 0.7790 (t80) cc_final: 0.7347 (t80) REVERT: D 174 MET cc_start: 0.4745 (mmm) cc_final: 0.4062 (mmm) REVERT: D 205 LYS cc_start: 0.7853 (tptt) cc_final: 0.6411 (mtpp) REVERT: D 263 THR cc_start: 0.7837 (p) cc_final: 0.7598 (p) REVERT: E 171 PHE cc_start: 0.7792 (t80) cc_final: 0.7090 (t80) REVERT: E 174 MET cc_start: 0.4973 (mmm) cc_final: 0.4440 (mmm) REVERT: E 293 ASN cc_start: 0.6184 (t0) cc_final: 0.5969 (m-40) REVERT: G 50 LYS cc_start: 0.6943 (mmmt) cc_final: 0.6674 (mtpt) REVERT: G 171 PHE cc_start: 0.7794 (t80) cc_final: 0.7545 (t80) REVERT: G 234 MET cc_start: 0.6367 (mtm) cc_final: 0.6127 (mtm) REVERT: G 260 TRP cc_start: 0.6939 (t60) cc_final: 0.6571 (t60) REVERT: G 293 ASN cc_start: 0.5723 (t0) cc_final: 0.5512 (m-40) outliers start: 102 outliers final: 64 residues processed: 347 average time/residue: 0.1039 time to fit residues: 57.0155 Evaluate side-chains 304 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 242 GLN F 293 ASN A 150 GLN A 173 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 176 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.181736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.148891 restraints weight = 26404.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.152128 restraints weight = 17612.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.154169 restraints weight = 13700.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.155423 restraints weight = 11734.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.156047 restraints weight = 10673.630| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16338 Z= 0.142 Angle : 0.650 15.391 22106 Z= 0.334 Chirality : 0.044 0.162 2352 Planarity : 0.003 0.035 2849 Dihedral : 6.232 49.412 2173 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.50 % Allowed : 20.52 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.82 (0.19), residues: 1960 helix: None (None), residues: 0 sheet: -1.64 (0.18), residues: 812 loop : -2.07 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 281 TYR 0.018 0.001 TYR G 65 PHE 0.021 0.002 PHE G 196 TRP 0.040 0.002 TRP D 80 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00315 (16338) covalent geometry : angle 0.65000 (22106) hydrogen bonds : bond 0.03317 ( 408) hydrogen bonds : angle 7.48162 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 246 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 150 GLN cc_start: 0.6748 (pm20) cc_final: 0.6526 (pm20) REVERT: A 174 MET cc_start: 0.5131 (mmm) cc_final: 0.4755 (mmm) REVERT: A 205 LYS cc_start: 0.7449 (tptt) cc_final: 0.6095 (mtpp) REVERT: B 25 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6886 (tt) REVERT: B 92 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7433 (p0) REVERT: B 173 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.6820 (p0) REVERT: B 286 TRP cc_start: 0.7191 (m100) cc_final: 0.6950 (m100) REVERT: D 78 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8197 (tt) REVERT: D 158 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.3851 (tp30) REVERT: D 171 PHE cc_start: 0.7853 (t80) cc_final: 0.7389 (t80) REVERT: D 174 MET cc_start: 0.4370 (mmm) cc_final: 0.3917 (mmm) REVERT: E 70 GLU cc_start: 0.5738 (tt0) cc_final: 0.5377 (tt0) REVERT: E 171 PHE cc_start: 0.7957 (t80) cc_final: 0.7187 (t80) REVERT: E 174 MET cc_start: 0.4882 (mmm) cc_final: 0.4375 (mmm) REVERT: E 205 LYS cc_start: 0.7826 (tptt) cc_final: 0.6405 (tttm) REVERT: G 158 GLU cc_start: 0.4246 (OUTLIER) cc_final: 0.3963 (tp30) REVERT: G 171 PHE cc_start: 0.7948 (t80) cc_final: 0.7157 (t80) REVERT: G 293 ASN cc_start: 0.5931 (t0) cc_final: 0.5729 (m-40) outliers start: 97 outliers final: 71 residues processed: 332 average time/residue: 0.1011 time to fit residues: 52.5186 Evaluate side-chains 293 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 216 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 78 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 151 optimal weight: 0.0970 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.185800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.150674 restraints weight = 25751.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.153578 restraints weight = 18487.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.155414 restraints weight = 15055.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.156635 restraints weight = 13257.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.157380 restraints weight = 12231.208| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16338 Z= 0.229 Angle : 0.744 17.198 22106 Z= 0.384 Chirality : 0.047 0.162 2352 Planarity : 0.004 0.033 2849 Dihedral : 6.639 49.565 2173 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 5.84 % Allowed : 20.41 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -3.04 (0.19), residues: 1960 helix: None (None), residues: 0 sheet: -1.90 (0.17), residues: 826 loop : -2.11 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 184 TYR 0.027 0.002 TYR C 65 PHE 0.029 0.003 PHE G 196 TRP 0.029 0.002 TRP D 80 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00522 (16338) covalent geometry : angle 0.74393 (22106) hydrogen bonds : bond 0.03992 ( 408) hydrogen bonds : angle 7.94350 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 224 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 110 LYS cc_start: 0.7647 (mtmt) cc_final: 0.6927 (mtpp) REVERT: F 113 MET cc_start: 0.5647 (tpt) cc_final: 0.5170 (tpt) REVERT: F 150 GLN cc_start: 0.6920 (pm20) cc_final: 0.6628 (pm20) REVERT: F 174 MET cc_start: 0.4308 (mmm) cc_final: 0.4100 (mmm) REVERT: F 251 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7989 (ttp80) REVERT: A 147 LYS cc_start: 0.7678 (tppt) cc_final: 0.7151 (ttmm) REVERT: A 287 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: B 92 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7756 (p0) REVERT: B 113 MET cc_start: 0.2050 (mmm) cc_final: 0.1751 (mmm) REVERT: B 145 THR cc_start: 0.7862 (p) cc_final: 0.7650 (p) REVERT: B 174 MET cc_start: 0.4590 (mmm) cc_final: 0.4387 (mmm) REVERT: D 78 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8212 (tt) REVERT: D 158 GLU cc_start: 0.4235 (OUTLIER) cc_final: 0.3971 (tp30) REVERT: D 171 PHE cc_start: 0.7921 (t80) cc_final: 0.7676 (t80) REVERT: D 174 MET cc_start: 0.4338 (mmm) cc_final: 0.4087 (mmm) REVERT: E 25 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7162 (tt) REVERT: E 46 LYS cc_start: 0.7559 (mttt) cc_final: 0.7273 (mmmt) REVERT: E 171 PHE cc_start: 0.8102 (t80) cc_final: 0.7734 (t80) REVERT: E 174 MET cc_start: 0.5129 (mmm) cc_final: 0.4876 (mmm) REVERT: E 293 ASN cc_start: 0.6173 (OUTLIER) cc_final: 0.5806 (m110) REVERT: G 158 GLU cc_start: 0.4449 (OUTLIER) cc_final: 0.4064 (tp30) REVERT: G 171 PHE cc_start: 0.7863 (t80) cc_final: 0.7543 (t80) REVERT: G 210 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6531 (m-10) outliers start: 103 outliers final: 81 residues processed: 319 average time/residue: 0.1089 time to fit residues: 54.5627 Evaluate side-chains 300 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 210 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 224 PHE Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 180 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN D 176 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.183352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.150825 restraints weight = 26142.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.154163 restraints weight = 17249.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.156262 restraints weight = 13312.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.157609 restraints weight = 11349.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.158486 restraints weight = 10270.069| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16338 Z= 0.127 Angle : 0.674 15.027 22106 Z= 0.343 Chirality : 0.045 0.196 2352 Planarity : 0.003 0.033 2849 Dihedral : 6.163 50.183 2173 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.59 % Allowed : 21.66 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.72 (0.19), residues: 1960 helix: None (None), residues: 0 sheet: -1.61 (0.18), residues: 819 loop : -1.96 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 281 TYR 0.015 0.001 TYR F 112 PHE 0.025 0.002 PHE B 171 TRP 0.028 0.001 TRP D 80 HIS 0.002 0.000 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00279 (16338) covalent geometry : angle 0.67422 (22106) hydrogen bonds : bond 0.03155 ( 408) hydrogen bonds : angle 7.31240 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 232 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 112 TYR cc_start: 0.6341 (t80) cc_final: 0.6001 (t80) REVERT: F 113 MET cc_start: 0.5860 (tpt) cc_final: 0.5458 (tpt) REVERT: A 147 LYS cc_start: 0.7476 (tppt) cc_final: 0.6867 (ttmm) REVERT: B 25 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6801 (tt) REVERT: B 92 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7465 (p0) REVERT: B 174 MET cc_start: 0.4477 (mmm) cc_final: 0.3884 (mmm) REVERT: D 158 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.3855 (tp30) REVERT: D 171 PHE cc_start: 0.7707 (t80) cc_final: 0.7320 (t80) REVERT: D 174 MET cc_start: 0.4045 (mmm) cc_final: 0.3609 (mmm) REVERT: E 46 LYS cc_start: 0.7370 (mttt) cc_final: 0.7170 (mmmt) REVERT: E 171 PHE cc_start: 0.7943 (t80) cc_final: 0.7240 (t80) REVERT: E 174 MET cc_start: 0.4687 (mmm) cc_final: 0.4387 (mmm) REVERT: E 196 PHE cc_start: 0.6913 (m-10) cc_final: 0.6623 (m-10) REVERT: E 293 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5895 (m110) REVERT: G 158 GLU cc_start: 0.4002 (OUTLIER) cc_final: 0.3742 (tp30) REVERT: G 171 PHE cc_start: 0.7729 (t80) cc_final: 0.7342 (t80) REVERT: G 210 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6601 (m-10) outliers start: 81 outliers final: 64 residues processed: 309 average time/residue: 0.1116 time to fit residues: 54.3609 Evaluate side-chains 285 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 0.0050 chunk 31 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.182257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.150372 restraints weight = 26608.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.153254 restraints weight = 18439.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.155046 restraints weight = 14706.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.156181 restraints weight = 12829.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.156741 restraints weight = 11782.150| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16338 Z= 0.256 Angle : 0.799 16.555 22106 Z= 0.412 Chirality : 0.048 0.262 2352 Planarity : 0.004 0.033 2849 Dihedral : 6.813 53.578 2173 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.10 % Allowed : 22.39 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.10 (0.19), residues: 1960 helix: None (None), residues: 0 sheet: -1.93 (0.18), residues: 812 loop : -2.18 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 184 TYR 0.032 0.002 TYR C 65 PHE 0.037 0.003 PHE F 196 TRP 0.037 0.002 TRP A 286 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00588 (16338) covalent geometry : angle 0.79943 (22106) hydrogen bonds : bond 0.04240 ( 408) hydrogen bonds : angle 8.01530 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 221 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 251 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8064 (ttp80) REVERT: A 147 LYS cc_start: 0.7665 (tppt) cc_final: 0.7142 (ttmm) REVERT: A 174 MET cc_start: 0.5390 (mmm) cc_final: 0.5155 (mmm) REVERT: B 75 LYS cc_start: 0.6430 (ttmm) cc_final: 0.5732 (tptt) REVERT: B 92 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7792 (p0) REVERT: C 50 LYS cc_start: 0.6855 (mmmt) cc_final: 0.6423 (mtpt) REVERT: C 260 TRP cc_start: 0.6821 (t60) cc_final: 0.6601 (t60) REVERT: D 78 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8175 (tt) REVERT: D 158 GLU cc_start: 0.4322 (OUTLIER) cc_final: 0.4053 (tp30) REVERT: D 171 PHE cc_start: 0.8041 (t80) cc_final: 0.7718 (t80) REVERT: D 174 MET cc_start: 0.4393 (mmm) cc_final: 0.4140 (mmm) REVERT: E 46 LYS cc_start: 0.7535 (mttt) cc_final: 0.7269 (mmmt) REVERT: E 171 PHE cc_start: 0.8114 (t80) cc_final: 0.7725 (t80) REVERT: E 174 MET cc_start: 0.5002 (mmm) cc_final: 0.4581 (mmm) REVERT: G 50 LYS cc_start: 0.6584 (mmmt) cc_final: 0.6276 (mtpt) REVERT: G 158 GLU cc_start: 0.4444 (OUTLIER) cc_final: 0.4038 (tp30) REVERT: G 171 PHE cc_start: 0.7898 (t80) cc_final: 0.6752 (t80) REVERT: G 174 MET cc_start: 0.5695 (mmm) cc_final: 0.4903 (mmm) REVERT: G 210 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6458 (m-10) outliers start: 90 outliers final: 70 residues processed: 302 average time/residue: 0.1083 time to fit residues: 51.9575 Evaluate side-chains 284 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 224 PHE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 37 optimal weight: 0.3980 chunk 101 optimal weight: 0.0020 chunk 135 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 150 GLN F 264 ASN A 173 ASN B 173 ASN B 242 GLN D 6 ASN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.185192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.153063 restraints weight = 25159.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.156647 restraints weight = 16055.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.158910 restraints weight = 12086.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.160390 restraints weight = 10148.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.161349 restraints weight = 9077.866| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16338 Z= 0.124 Angle : 0.692 15.212 22106 Z= 0.354 Chirality : 0.045 0.181 2352 Planarity : 0.003 0.033 2849 Dihedral : 6.234 53.395 2173 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.85 % Allowed : 23.47 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.91 (0.19), residues: 1960 helix: -1.96 (0.72), residues: 42 sheet: -1.76 (0.18), residues: 875 loop : -2.04 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 281 TYR 0.015 0.001 TYR F 112 PHE 0.022 0.002 PHE F 196 TRP 0.039 0.002 TRP A 286 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00273 (16338) covalent geometry : angle 0.69201 (22106) hydrogen bonds : bond 0.03356 ( 408) hydrogen bonds : angle 7.25994 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 112 TYR cc_start: 0.6429 (t80) cc_final: 0.6170 (t80) REVERT: F 171 PHE cc_start: 0.7492 (t80) cc_final: 0.7193 (t80) REVERT: F 174 MET cc_start: 0.4865 (mmm) cc_final: 0.4317 (mmm) REVERT: A 147 LYS cc_start: 0.7494 (tppt) cc_final: 0.6941 (ttmm) REVERT: B 92 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7491 (p0) REVERT: B 174 MET cc_start: 0.4763 (mmm) cc_final: 0.4137 (mmm) REVERT: B 260 TRP cc_start: 0.6858 (t60) cc_final: 0.6447 (t60) REVERT: C 50 LYS cc_start: 0.6763 (mmmt) cc_final: 0.6246 (mtpt) REVERT: D 158 GLU cc_start: 0.4065 (OUTLIER) cc_final: 0.3823 (tp30) REVERT: D 171 PHE cc_start: 0.7812 (t80) cc_final: 0.7403 (t80) REVERT: D 174 MET cc_start: 0.4129 (mmm) cc_final: 0.3681 (mmm) REVERT: D 291 MET cc_start: 0.5620 (ttt) cc_final: 0.5148 (ttt) REVERT: E 46 LYS cc_start: 0.7475 (mttt) cc_final: 0.7252 (mmmt) REVERT: E 171 PHE cc_start: 0.7805 (t80) cc_final: 0.7419 (t80) REVERT: E 174 MET cc_start: 0.4836 (mmm) cc_final: 0.4352 (mmm) REVERT: G 171 PHE cc_start: 0.7792 (t80) cc_final: 0.6537 (t80) REVERT: G 174 MET cc_start: 0.5406 (mmm) cc_final: 0.4506 (mmm) REVERT: G 210 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6319 (m-10) outliers start: 68 outliers final: 55 residues processed: 305 average time/residue: 0.1040 time to fit residues: 50.1917 Evaluate side-chains 266 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 76 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 150 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.183009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.150939 restraints weight = 25436.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.154381 restraints weight = 16397.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.156577 restraints weight = 12458.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.158031 restraints weight = 10511.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.159001 restraints weight = 9423.689| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16338 Z= 0.138 Angle : 0.710 14.658 22106 Z= 0.362 Chirality : 0.045 0.154 2352 Planarity : 0.003 0.032 2849 Dihedral : 6.130 53.884 2170 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.68 % Allowed : 24.55 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.88 (0.19), residues: 1960 helix: -2.17 (0.67), residues: 42 sheet: -1.83 (0.17), residues: 896 loop : -1.91 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 104 TYR 0.017 0.001 TYR F 65 PHE 0.027 0.002 PHE E 196 TRP 0.053 0.002 TRP D 80 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00310 (16338) covalent geometry : angle 0.71023 (22106) hydrogen bonds : bond 0.03404 ( 408) hydrogen bonds : angle 7.15920 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.30 seconds wall clock time: 48 minutes 53.08 seconds (2933.08 seconds total)