Starting phenix.real_space_refine on Thu Mar 5 09:42:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qd2_4517/03_2026/6qd2_4517.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd2_4517/03_2026/6qd2_4517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qd2_4517/03_2026/6qd2_4517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd2_4517/03_2026/6qd2_4517.map" model { file = "/net/cci-nas-00/data/ceres_data/6qd2_4517/03_2026/6qd2_4517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd2_4517/03_2026/6qd2_4517.cif" } resolution = 4.8 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= 1.000 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 44 5.16 5 C 6936 2.51 5 N 1820 2.21 5 O 1844 1.98 5 H 11100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "D" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.95, per 1000 atoms: 0.18 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 102.7, 94.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 44 16.00 O 1844 8.00 N 1820 7.00 C 6936 6.00 H 11100 1.00 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: 2.01 Conformation dependent library (CDL) restraints added in 470.4 milliseconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 64.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.535A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 34 through 61 removed outlier: 3.544A pdb=" N ARG A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.585A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.241A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 186 through 192 removed outlier: 4.042A pdb=" N ALA A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 225 removed outlier: 4.083A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.973A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.021A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.536A pdb=" N LEU B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.543A pdb=" N ARG B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 3.586A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.241A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 192 removed outlier: 4.042A pdb=" N ALA B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 225 removed outlier: 4.084A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.974A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 334 through 354 removed outlier: 4.021A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.535A pdb=" N LEU C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 29' Processing helix chain 'C' and resid 34 through 61 removed outlier: 3.543A pdb=" N ARG C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.585A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.241A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 186 through 192 removed outlier: 4.042A pdb=" N ALA C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 225 removed outlier: 4.083A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.974A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.021A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.535A pdb=" N LEU D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 29 " --> pdb=" O VAL D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.543A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.925A pdb=" N VAL D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.586A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.240A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 152 removed outlier: 4.047A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 186 through 192 removed outlier: 4.041A pdb=" N ALA D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 225 removed outlier: 4.083A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.973A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.022A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 256 removed outlier: 4.210A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 removed outlier: 4.177A pdb=" N THR A 310 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 254 through 256 removed outlier: 4.210A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 261 through 263 removed outlier: 4.178A pdb=" N THR B 310 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 254 through 256 removed outlier: 4.209A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 261 through 263 removed outlier: 4.177A pdb=" N THR C 310 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 254 through 256 removed outlier: 4.210A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 261 through 263 removed outlier: 4.178A pdb=" N THR D 310 " --> pdb=" O ALA D 283 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1464 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: 5.14 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11088 1.03 - 1.22: 12 1.22 - 1.42: 4343 1.42 - 1.61: 6461 1.61 - 1.81: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" CZ ARG C 220 " pdb=" NH2 ARG C 220 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.23e+00 bond pdb=" CZ ARG B 220 " pdb=" NH2 ARG B 220 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.23e+00 bond pdb=" CZ ARG D 220 " pdb=" NH2 ARG D 220 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.06e+00 bond pdb=" CZ ARG A 220 " pdb=" NH2 ARG A 220 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" CB TRP A 167 " pdb=" CG TRP A 167 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.60e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 37674 1.62 - 3.25: 2026 3.25 - 4.87: 185 4.87 - 6.50: 49 6.50 - 8.12: 6 Bond angle restraints: 39940 Sorted by residual: angle pdb=" C ALA D 11 " pdb=" CA ALA D 11 " pdb=" CB ALA D 11 " ideal model delta sigma weight residual 113.57 108.63 4.94 1.57e+00 4.06e-01 9.89e+00 angle pdb=" C ALA C 11 " pdb=" CA ALA C 11 " pdb=" CB ALA C 11 " ideal model delta sigma weight residual 113.57 108.64 4.93 1.57e+00 4.06e-01 9.85e+00 angle pdb=" C ALA B 11 " pdb=" CA ALA B 11 " pdb=" CB ALA B 11 " ideal model delta sigma weight residual 113.57 108.66 4.91 1.57e+00 4.06e-01 9.79e+00 angle pdb=" C ALA A 11 " pdb=" CA ALA A 11 " pdb=" CB ALA A 11 " ideal model delta sigma weight residual 113.57 108.70 4.87 1.57e+00 4.06e-01 9.61e+00 angle pdb=" CG HIS D 323 " pdb=" CB HIS D 323 " pdb=" HB3 HIS D 323 " ideal model delta sigma weight residual 108.00 99.88 8.12 3.00e+00 1.11e-01 7.33e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 9559 15.07 - 30.14: 450 30.14 - 45.21: 171 45.21 - 60.28: 100 60.28 - 75.35: 8 Dihedral angle restraints: 10288 sinusoidal: 5604 harmonic: 4684 Sorted by residual: dihedral pdb=" CA SER B 112 " pdb=" C SER B 112 " pdb=" N THR B 113 " pdb=" CA THR B 113 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA SER D 112 " pdb=" C SER D 112 " pdb=" N THR D 113 " pdb=" CA THR D 113 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N THR C 113 " pdb=" CA THR C 113 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 10285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1052 0.030 - 0.060: 435 0.060 - 0.090: 205 0.090 - 0.121: 71 0.121 - 0.151: 21 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA VAL C 68 " pdb=" N VAL C 68 " pdb=" C VAL C 68 " pdb=" CB VAL C 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA VAL A 68 " pdb=" N VAL A 68 " pdb=" C VAL A 68 " pdb=" CB VAL A 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA VAL D 68 " pdb=" N VAL D 68 " pdb=" C VAL D 68 " pdb=" CB VAL D 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.011 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" N ALA A 325 " -0.034 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 30 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO C 31 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 30 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO A 31 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.024 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.38: 8888 2.38 - 3.07: 63279 3.07 - 3.76: 72581 3.76 - 4.45: 112631 4.45 - 5.14: 171226 Nonbonded interactions: 428605 Sorted by model distance: nonbonded pdb=" O LYS A 62 " pdb="HH22 ARG A 69 " model vdw 1.686 2.450 nonbonded pdb=" O LYS C 62 " pdb="HH22 ARG C 69 " model vdw 1.687 2.450 nonbonded pdb=" O LYS B 62 " pdb="HH22 ARG B 69 " model vdw 1.687 2.450 nonbonded pdb=" O LYS D 62 " pdb="HH22 ARG D 69 " model vdw 1.687 2.450 nonbonded pdb="HH11 ARG B 120 " pdb=" OE2 GLU B 217 " model vdw 1.701 2.450 ... (remaining 428600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 355) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.050 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 : 0.006 0.046 10880 Z= 0.271 Angle : 0.857 6.874 14852 Z= 0.468 Chirality : 0.043 0.151 1784 Planarity : 0.006 0.044 1872 Dihedral : 9.036 75.347 3844 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.19), residues: 1412 helix: -3.82 (0.12), residues: 616 sheet: -4.07 (0.54), residues: 40 loop : -2.26 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 63 TYR 0.016 0.003 TYR C 10 PHE 0.015 0.002 PHE A 236 TRP 0.015 0.002 TRP A 167 HIS 0.005 0.003 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00596 (10880) covalent geometry : angle 0.85669 (14852) hydrogen bonds : bond 0.32501 ( 528) hydrogen bonds : angle 12.00678 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7644 (m-30) cc_final: 0.7420 (m-30) REVERT: A 227 TRP cc_start: 0.7345 (t60) cc_final: 0.6917 (t60) REVERT: B 36 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7105 (mtm180) REVERT: B 78 ASP cc_start: 0.7648 (m-30) cc_final: 0.7405 (m-30) REVERT: B 133 THR cc_start: 0.6578 (m) cc_final: 0.6376 (m) REVERT: B 151 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 227 TRP cc_start: 0.7407 (t60) cc_final: 0.6855 (t60) REVERT: C 36 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7160 (mtm180) REVERT: C 78 ASP cc_start: 0.7709 (m-30) cc_final: 0.7470 (m-30) REVERT: C 133 THR cc_start: 0.6595 (m) cc_final: 0.6367 (m) REVERT: C 151 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7540 (mm-30) REVERT: C 197 MET cc_start: 0.8752 (ttm) cc_final: 0.8060 (tpp) REVERT: C 227 TRP cc_start: 0.7499 (t60) cc_final: 0.7014 (t60) REVERT: D 227 TRP cc_start: 0.7546 (t60) cc_final: 0.7073 (t60) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2525 time to fit residues: 127.5963 Evaluate side-chains 303 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.237208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.203504 restraints weight = 60578.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.209395 restraints weight = 36646.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.213404 restraints weight = 25052.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.216239 restraints weight = 18728.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.218150 restraints weight = 14882.959| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10880 Z= 0.201 Angle : 0.704 7.486 14852 Z= 0.381 Chirality : 0.041 0.134 1784 Planarity : 0.007 0.038 1872 Dihedral : 6.173 23.128 1536 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.21), residues: 1412 helix: -2.42 (0.15), residues: 724 sheet: None (None), residues: 0 loop : -2.00 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.009 0.002 TYR C 178 PHE 0.011 0.001 PHE D 214 TRP 0.007 0.001 TRP A 104 HIS 0.004 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00392 (10880) covalent geometry : angle 0.70377 (14852) hydrogen bonds : bond 0.06751 ( 528) hydrogen bonds : angle 7.32032 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9212 (mt) cc_final: 0.8929 (tp) REVERT: A 133 THR cc_start: 0.7064 (m) cc_final: 0.6841 (m) REVERT: A 227 TRP cc_start: 0.6405 (t60) cc_final: 0.6056 (t60) REVERT: B 17 LEU cc_start: 0.9214 (mt) cc_final: 0.8922 (tp) REVERT: B 182 ILE cc_start: 0.7504 (mm) cc_final: 0.7198 (tp) REVERT: B 197 MET cc_start: 0.8300 (ttm) cc_final: 0.7741 (tpp) REVERT: B 214 PHE cc_start: 0.9005 (t80) cc_final: 0.8707 (t80) REVERT: B 227 TRP cc_start: 0.6281 (t60) cc_final: 0.5923 (t60) REVERT: C 17 LEU cc_start: 0.9217 (mt) cc_final: 0.8874 (tp) REVERT: C 180 ASP cc_start: 0.7930 (p0) cc_final: 0.7716 (p0) REVERT: C 197 MET cc_start: 0.8325 (ttm) cc_final: 0.7773 (tpp) REVERT: C 214 PHE cc_start: 0.9125 (t80) cc_final: 0.8804 (t80) REVERT: D 17 LEU cc_start: 0.9142 (mt) cc_final: 0.8841 (tp) REVERT: D 158 LYS cc_start: 0.9234 (mptt) cc_final: 0.9022 (mmmt) REVERT: D 197 MET cc_start: 0.8184 (ttm) cc_final: 0.7601 (tpp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2149 time to fit residues: 103.6632 Evaluate side-chains 304 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 20.0000 chunk 136 optimal weight: 50.0000 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.231418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.197145 restraints weight = 61937.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.203033 restraints weight = 36426.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.206816 restraints weight = 24118.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.209794 restraints weight = 17868.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.212135 restraints weight = 14429.955| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10880 Z= 0.185 Angle : 0.639 5.601 14852 Z= 0.347 Chirality : 0.039 0.130 1784 Planarity : 0.006 0.071 1872 Dihedral : 5.752 21.837 1536 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.21), residues: 1412 helix: -1.63 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 264 TYR 0.011 0.002 TYR C 178 PHE 0.011 0.002 PHE D 223 TRP 0.008 0.001 TRP A 167 HIS 0.014 0.006 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00361 (10880) covalent geometry : angle 0.63919 (14852) hydrogen bonds : bond 0.05691 ( 528) hydrogen bonds : angle 6.42116 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9264 (mt) cc_final: 0.8824 (tp) REVERT: A 101 CYS cc_start: 0.8135 (m) cc_final: 0.7837 (m) REVERT: A 133 THR cc_start: 0.6482 (m) cc_final: 0.6279 (m) REVERT: A 197 MET cc_start: 0.8385 (ttm) cc_final: 0.7945 (tpp) REVERT: A 214 PHE cc_start: 0.9174 (t80) cc_final: 0.8948 (t80) REVERT: A 281 SER cc_start: 0.7331 (t) cc_final: 0.6994 (m) REVERT: B 13 LEU cc_start: 0.8276 (mt) cc_final: 0.8017 (mt) REVERT: B 17 LEU cc_start: 0.9266 (mt) cc_final: 0.8760 (tp) REVERT: B 101 CYS cc_start: 0.7998 (m) cc_final: 0.7636 (m) REVERT: B 133 THR cc_start: 0.6415 (m) cc_final: 0.6207 (m) REVERT: B 182 ILE cc_start: 0.7467 (mm) cc_final: 0.6785 (tp) REVERT: B 197 MET cc_start: 0.8347 (ttm) cc_final: 0.7861 (tpp) REVERT: B 214 PHE cc_start: 0.8976 (t80) cc_final: 0.8607 (t80) REVERT: B 281 SER cc_start: 0.6526 (t) cc_final: 0.6116 (m) REVERT: C 13 LEU cc_start: 0.8255 (mt) cc_final: 0.8000 (mt) REVERT: C 17 LEU cc_start: 0.9241 (mt) cc_final: 0.8731 (tp) REVERT: C 101 CYS cc_start: 0.7966 (m) cc_final: 0.7644 (m) REVERT: C 196 MET cc_start: 0.8176 (mpp) cc_final: 0.7946 (mmt) REVERT: C 197 MET cc_start: 0.8295 (ttm) cc_final: 0.7796 (tpp) REVERT: C 214 PHE cc_start: 0.9050 (t80) cc_final: 0.8753 (t80) REVERT: D 13 LEU cc_start: 0.8260 (mt) cc_final: 0.8055 (mt) REVERT: D 17 LEU cc_start: 0.9262 (mt) cc_final: 0.8814 (tp) REVERT: D 101 CYS cc_start: 0.7991 (m) cc_final: 0.7731 (m) REVERT: D 133 THR cc_start: 0.6510 (m) cc_final: 0.6293 (m) REVERT: D 196 MET cc_start: 0.8130 (mpp) cc_final: 0.7700 (mmt) REVERT: D 197 MET cc_start: 0.8212 (ttm) cc_final: 0.7723 (tpp) REVERT: D 281 SER cc_start: 0.7504 (t) cc_final: 0.7076 (m) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1898 time to fit residues: 86.0829 Evaluate side-chains 288 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.229243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.190428 restraints weight = 63182.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.197088 restraints weight = 34410.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.201139 restraints weight = 22106.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.204602 restraints weight = 16331.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.205843 restraints weight = 12770.893| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10880 Z= 0.166 Angle : 0.597 5.872 14852 Z= 0.324 Chirality : 0.038 0.124 1784 Planarity : 0.006 0.086 1872 Dihedral : 5.386 19.551 1536 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.22), residues: 1412 helix: -1.18 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -2.30 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 220 TYR 0.009 0.002 TYR C 215 PHE 0.014 0.001 PHE A 223 TRP 0.009 0.001 TRP A 206 HIS 0.012 0.006 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00326 (10880) covalent geometry : angle 0.59657 (14852) hydrogen bonds : bond 0.04822 ( 528) hydrogen bonds : angle 5.97597 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9262 (mt) cc_final: 0.8930 (tp) REVERT: A 101 CYS cc_start: 0.8389 (m) cc_final: 0.7994 (m) REVERT: A 197 MET cc_start: 0.8627 (ttm) cc_final: 0.8210 (tpp) REVERT: A 214 PHE cc_start: 0.9348 (t80) cc_final: 0.9101 (t80) REVERT: A 227 TRP cc_start: 0.7014 (t60) cc_final: 0.6806 (t60) REVERT: A 281 SER cc_start: 0.7407 (t) cc_final: 0.7053 (m) REVERT: A 323 HIS cc_start: 0.3452 (m-70) cc_final: 0.3247 (m-70) REVERT: A 346 LEU cc_start: 0.7919 (tt) cc_final: 0.7697 (tt) REVERT: B 17 LEU cc_start: 0.9275 (mt) cc_final: 0.8878 (tp) REVERT: B 101 CYS cc_start: 0.8302 (m) cc_final: 0.7904 (m) REVERT: B 182 ILE cc_start: 0.7590 (mm) cc_final: 0.6747 (tp) REVERT: B 197 MET cc_start: 0.8574 (ttm) cc_final: 0.8135 (tpp) REVERT: B 214 PHE cc_start: 0.9061 (t80) cc_final: 0.8768 (t80) REVERT: B 227 TRP cc_start: 0.7014 (t60) cc_final: 0.6694 (t60) REVERT: B 281 SER cc_start: 0.6965 (t) cc_final: 0.6479 (m) REVERT: C 17 LEU cc_start: 0.9254 (mt) cc_final: 0.8887 (tp) REVERT: C 36 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7172 (mtm180) REVERT: C 100 TYR cc_start: 0.7874 (m-80) cc_final: 0.7655 (m-80) REVERT: C 101 CYS cc_start: 0.8328 (m) cc_final: 0.7967 (m) REVERT: C 196 MET cc_start: 0.8452 (mpp) cc_final: 0.8195 (mmt) REVERT: C 197 MET cc_start: 0.8560 (ttm) cc_final: 0.8115 (tpp) REVERT: C 214 PHE cc_start: 0.9209 (t80) cc_final: 0.8951 (t80) REVERT: C 227 TRP cc_start: 0.7100 (t60) cc_final: 0.6811 (t60) REVERT: D 17 LEU cc_start: 0.9281 (mt) cc_final: 0.8921 (tp) REVERT: D 101 CYS cc_start: 0.8379 (m) cc_final: 0.8078 (m) REVERT: D 107 LYS cc_start: 0.9306 (mmmt) cc_final: 0.9078 (tppp) REVERT: D 196 MET cc_start: 0.8287 (mpp) cc_final: 0.8082 (mmt) REVERT: D 197 MET cc_start: 0.8563 (ttm) cc_final: 0.8182 (tpp) REVERT: D 227 TRP cc_start: 0.6988 (t60) cc_final: 0.6698 (t60) REVERT: D 281 SER cc_start: 0.7672 (t) cc_final: 0.7202 (m) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1856 time to fit residues: 82.3185 Evaluate side-chains 279 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 237 GLN C 237 GLN D 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.226599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.185946 restraints weight = 62561.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.193175 restraints weight = 33020.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.197438 restraints weight = 20767.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.200061 restraints weight = 14831.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.203022 restraints weight = 11919.904| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10880 Z= 0.149 Angle : 0.580 5.654 14852 Z= 0.311 Chirality : 0.038 0.127 1784 Planarity : 0.005 0.056 1872 Dihedral : 5.117 17.332 1536 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.22), residues: 1412 helix: -0.81 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 220 TYR 0.011 0.002 TYR C 52 PHE 0.016 0.001 PHE A 223 TRP 0.009 0.001 TRP B 104 HIS 0.017 0.006 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00301 (10880) covalent geometry : angle 0.57981 (14852) hydrogen bonds : bond 0.04476 ( 528) hydrogen bonds : angle 5.63254 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9328 (mt) cc_final: 0.8907 (tp) REVERT: A 92 ASP cc_start: 0.6409 (t0) cc_final: 0.6110 (t0) REVERT: A 101 CYS cc_start: 0.8351 (m) cc_final: 0.7985 (m) REVERT: A 197 MET cc_start: 0.8557 (ttm) cc_final: 0.8267 (tpp) REVERT: A 214 PHE cc_start: 0.9359 (t80) cc_final: 0.9081 (t80) REVERT: A 281 SER cc_start: 0.6800 (t) cc_final: 0.6537 (m) REVERT: A 323 HIS cc_start: 0.4945 (m-70) cc_final: 0.4663 (m-70) REVERT: B 17 LEU cc_start: 0.9292 (mt) cc_final: 0.8675 (tp) REVERT: B 25 VAL cc_start: 0.8643 (t) cc_final: 0.8292 (p) REVERT: B 48 ILE cc_start: 0.9502 (mt) cc_final: 0.9114 (mt) REVERT: B 182 ILE cc_start: 0.7630 (mm) cc_final: 0.7056 (tp) REVERT: B 197 MET cc_start: 0.8567 (ttm) cc_final: 0.8240 (tpp) REVERT: B 214 PHE cc_start: 0.9025 (t80) cc_final: 0.8739 (t80) REVERT: B 227 TRP cc_start: 0.6925 (t60) cc_final: 0.6674 (t60) REVERT: B 281 SER cc_start: 0.6907 (t) cc_final: 0.6504 (m) REVERT: C 17 LEU cc_start: 0.9255 (mt) cc_final: 0.8837 (tp) REVERT: C 25 VAL cc_start: 0.8636 (t) cc_final: 0.8225 (p) REVERT: C 36 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7073 (mtm180) REVERT: C 96 ASP cc_start: 0.7374 (m-30) cc_final: 0.7157 (p0) REVERT: C 100 TYR cc_start: 0.7871 (m-80) cc_final: 0.7611 (m-80) REVERT: C 133 THR cc_start: 0.6684 (m) cc_final: 0.6467 (m) REVERT: C 197 MET cc_start: 0.8552 (ttm) cc_final: 0.8190 (tpp) REVERT: C 214 PHE cc_start: 0.9183 (t80) cc_final: 0.8896 (t80) REVERT: C 223 PHE cc_start: 0.7035 (t80) cc_final: 0.6815 (t80) REVERT: C 227 TRP cc_start: 0.7019 (t60) cc_final: 0.6794 (t60) REVERT: D 92 ASP cc_start: 0.6442 (t0) cc_final: 0.6119 (t0) REVERT: D 107 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8953 (tppp) REVERT: D 133 THR cc_start: 0.6717 (m) cc_final: 0.6502 (m) REVERT: D 196 MET cc_start: 0.8172 (mpp) cc_final: 0.7964 (mmt) REVERT: D 197 MET cc_start: 0.8541 (ttm) cc_final: 0.8249 (tpp) REVERT: D 281 SER cc_start: 0.7562 (t) cc_final: 0.7187 (m) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1796 time to fit residues: 78.2103 Evaluate side-chains 285 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 31 optimal weight: 40.0000 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.227221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188518 restraints weight = 64244.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.194497 restraints weight = 36116.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.198126 restraints weight = 23907.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.200701 restraints weight = 17711.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.202203 restraints weight = 14287.614| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 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 : 0.003 0.029 10880 Z= 0.147 Angle : 0.565 5.415 14852 Z= 0.303 Chirality : 0.038 0.121 1784 Planarity : 0.005 0.056 1872 Dihedral : 4.933 18.043 1536 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.22), residues: 1412 helix: -0.61 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -2.11 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.007 0.001 TYR A 100 PHE 0.017 0.001 PHE A 223 TRP 0.011 0.001 TRP A 227 HIS 0.012 0.005 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00291 (10880) covalent geometry : angle 0.56510 (14852) hydrogen bonds : bond 0.04240 ( 528) hydrogen bonds : angle 5.38893 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.8686 (t) cc_final: 0.8405 (p) REVERT: A 133 THR cc_start: 0.6784 (m) cc_final: 0.6560 (m) REVERT: A 197 MET cc_start: 0.8477 (ttm) cc_final: 0.8244 (tpp) REVERT: A 281 SER cc_start: 0.6655 (t) cc_final: 0.6377 (m) REVERT: B 13 LEU cc_start: 0.8359 (mt) cc_final: 0.8129 (mt) REVERT: B 17 LEU cc_start: 0.9288 (mt) cc_final: 0.8771 (tp) REVERT: B 74 LYS cc_start: 0.9153 (ttmt) cc_final: 0.8848 (mtmm) REVERT: B 133 THR cc_start: 0.6778 (m) cc_final: 0.6566 (m) REVERT: B 182 ILE cc_start: 0.7634 (mm) cc_final: 0.7071 (tp) REVERT: B 214 PHE cc_start: 0.8996 (t80) cc_final: 0.8735 (t80) REVERT: B 281 SER cc_start: 0.7017 (t) cc_final: 0.6688 (m) REVERT: C 96 ASP cc_start: 0.7187 (m-30) cc_final: 0.6870 (p0) REVERT: C 133 THR cc_start: 0.6628 (m) cc_final: 0.6410 (m) REVERT: C 214 PHE cc_start: 0.9049 (t80) cc_final: 0.8780 (t80) REVERT: C 223 PHE cc_start: 0.7209 (t80) cc_final: 0.7002 (t80) REVERT: D 107 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8970 (tppp) REVERT: D 133 THR cc_start: 0.6784 (m) cc_final: 0.6558 (m) REVERT: D 197 MET cc_start: 0.8482 (ttm) cc_final: 0.8268 (tpp) REVERT: D 214 PHE cc_start: 0.9457 (t80) cc_final: 0.9194 (t80) REVERT: D 223 PHE cc_start: 0.7290 (t80) cc_final: 0.7069 (t80) REVERT: D 281 SER cc_start: 0.7465 (t) cc_final: 0.7065 (m) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1637 time to fit residues: 73.8588 Evaluate side-chains 278 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.224645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.184273 restraints weight = 63325.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.191267 restraints weight = 33065.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.195597 restraints weight = 20754.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.198452 restraints weight = 14765.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.200326 restraints weight = 11563.645| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10880 Z= 0.146 Angle : 0.567 5.214 14852 Z= 0.305 Chirality : 0.038 0.122 1784 Planarity : 0.005 0.051 1872 Dihedral : 4.925 18.333 1536 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.22), residues: 1412 helix: -0.50 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -2.07 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.009 0.001 TYR C 100 PHE 0.017 0.001 PHE D 214 TRP 0.011 0.001 TRP C 206 HIS 0.012 0.007 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00291 (10880) covalent geometry : angle 0.56745 (14852) hydrogen bonds : bond 0.04176 ( 528) hydrogen bonds : angle 5.32503 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8978 (ttpt) REVERT: A 92 ASP cc_start: 0.4927 (t0) cc_final: 0.4709 (t0) REVERT: A 227 TRP cc_start: 0.7120 (t60) cc_final: 0.6919 (t60) REVERT: A 281 SER cc_start: 0.6688 (t) cc_final: 0.6408 (m) REVERT: B 74 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8949 (ttpt) REVERT: B 197 MET cc_start: 0.8205 (tpp) cc_final: 0.7876 (tpp) REVERT: B 214 PHE cc_start: 0.8998 (t80) cc_final: 0.8688 (t80) REVERT: B 227 TRP cc_start: 0.7202 (t60) cc_final: 0.6963 (t60) REVERT: B 281 SER cc_start: 0.6825 (t) cc_final: 0.6477 (m) REVERT: C 92 ASP cc_start: 0.6056 (t0) cc_final: 0.4283 (t0) REVERT: C 96 ASP cc_start: 0.7331 (m-30) cc_final: 0.6859 (p0) REVERT: C 133 THR cc_start: 0.6629 (m) cc_final: 0.6377 (m) REVERT: C 197 MET cc_start: 0.7971 (tpp) cc_final: 0.7585 (tpp) REVERT: C 227 TRP cc_start: 0.7224 (t60) cc_final: 0.7016 (t60) REVERT: C 281 SER cc_start: 0.7048 (t) cc_final: 0.6703 (m) REVERT: C 323 HIS cc_start: 0.5136 (m-70) cc_final: 0.4913 (m-70) REVERT: D 107 LYS cc_start: 0.9257 (mmmt) cc_final: 0.9009 (tppp) REVERT: D 133 THR cc_start: 0.6771 (m) cc_final: 0.6516 (m) REVERT: D 197 MET cc_start: 0.8491 (ttm) cc_final: 0.8249 (tpp) REVERT: D 214 PHE cc_start: 0.9400 (t80) cc_final: 0.9181 (t80) REVERT: D 281 SER cc_start: 0.7475 (t) cc_final: 0.7086 (m) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1668 time to fit residues: 74.9713 Evaluate side-chains 273 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 chunk 118 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.225566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.185415 restraints weight = 62930.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.192360 restraints weight = 32681.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.196642 restraints weight = 20547.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.199623 restraints weight = 14533.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.201549 restraints weight = 11359.965| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10880 Z= 0.128 Angle : 0.548 5.072 14852 Z= 0.291 Chirality : 0.038 0.120 1784 Planarity : 0.005 0.051 1872 Dihedral : 4.718 17.069 1536 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.22), residues: 1412 helix: -0.53 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -2.09 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.017 0.001 TYR D 178 PHE 0.015 0.001 PHE A 223 TRP 0.014 0.001 TRP B 206 HIS 0.009 0.004 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00264 (10880) covalent geometry : angle 0.54795 (14852) hydrogen bonds : bond 0.03922 ( 528) hydrogen bonds : angle 5.12142 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8926 (ttpt) REVERT: A 133 THR cc_start: 0.6635 (m) cc_final: 0.6428 (m) REVERT: A 197 MET cc_start: 0.8187 (tpp) cc_final: 0.7969 (tpp) REVERT: A 281 SER cc_start: 0.6642 (t) cc_final: 0.6401 (m) REVERT: B 74 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8916 (ttpt) REVERT: B 133 THR cc_start: 0.6728 (m) cc_final: 0.6458 (m) REVERT: B 214 PHE cc_start: 0.8867 (t80) cc_final: 0.8505 (t80) REVERT: B 227 TRP cc_start: 0.7038 (t60) cc_final: 0.6819 (t60) REVERT: C 92 ASP cc_start: 0.6142 (t0) cc_final: 0.5932 (t70) REVERT: C 133 THR cc_start: 0.6784 (m) cc_final: 0.6511 (m) REVERT: C 281 SER cc_start: 0.7027 (t) cc_final: 0.6714 (m) REVERT: C 323 HIS cc_start: 0.4950 (m-70) cc_final: 0.4709 (m-70) REVERT: D 107 LYS cc_start: 0.9253 (mmmt) cc_final: 0.9019 (tppp) REVERT: D 133 THR cc_start: 0.6742 (m) cc_final: 0.6504 (m) REVERT: D 214 PHE cc_start: 0.9351 (t80) cc_final: 0.9082 (t80) REVERT: D 281 SER cc_start: 0.7488 (t) cc_final: 0.7218 (m) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1629 time to fit residues: 73.1265 Evaluate side-chains 275 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 136 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 19 optimal weight: 20.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.227004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.184328 restraints weight = 63090.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.191217 restraints weight = 33471.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.195424 restraints weight = 20851.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.198122 restraints weight = 14997.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.199998 restraints weight = 12043.755| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10880 Z= 0.140 Angle : 0.563 5.231 14852 Z= 0.299 Chirality : 0.038 0.120 1784 Planarity : 0.005 0.055 1872 Dihedral : 4.740 17.662 1536 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.22), residues: 1412 helix: -0.58 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.013 0.001 TYR C 178 PHE 0.015 0.001 PHE A 223 TRP 0.014 0.002 TRP C 206 HIS 0.011 0.004 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00283 (10880) covalent geometry : angle 0.56254 (14852) hydrogen bonds : bond 0.03923 ( 528) hydrogen bonds : angle 5.08767 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8911 (ttpt) REVERT: A 133 THR cc_start: 0.6610 (m) cc_final: 0.6373 (m) REVERT: A 281 SER cc_start: 0.6771 (t) cc_final: 0.6505 (m) REVERT: B 74 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8938 (ttpt) REVERT: B 133 THR cc_start: 0.6708 (m) cc_final: 0.6458 (m) REVERT: B 214 PHE cc_start: 0.8985 (t80) cc_final: 0.8701 (t80) REVERT: B 281 SER cc_start: 0.7028 (t) cc_final: 0.6692 (m) REVERT: C 133 THR cc_start: 0.6734 (m) cc_final: 0.6517 (m) REVERT: C 148 TYR cc_start: 0.8046 (t80) cc_final: 0.7770 (t80) REVERT: C 214 PHE cc_start: 0.9104 (t80) cc_final: 0.8729 (t80) REVERT: C 281 SER cc_start: 0.7187 (t) cc_final: 0.6913 (m) REVERT: C 323 HIS cc_start: 0.5070 (m-70) cc_final: 0.4821 (m-70) REVERT: D 197 MET cc_start: 0.7869 (tpp) cc_final: 0.7624 (tpp) REVERT: D 214 PHE cc_start: 0.9374 (t80) cc_final: 0.9078 (t80) REVERT: D 281 SER cc_start: 0.7539 (t) cc_final: 0.7281 (m) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1630 time to fit residues: 71.6868 Evaluate side-chains 269 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 0.0270 chunk 127 optimal weight: 0.0070 chunk 139 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 overall best weight: 4.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.225369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.185584 restraints weight = 63088.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.192423 restraints weight = 33303.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196665 restraints weight = 21008.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.199425 restraints weight = 15029.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.201273 restraints weight = 11809.798| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10880 Z= 0.115 Angle : 0.536 4.882 14852 Z= 0.282 Chirality : 0.038 0.119 1784 Planarity : 0.004 0.050 1872 Dihedral : 4.578 16.969 1536 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1412 helix: -0.32 (0.19), residues: 832 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.009 0.001 TYR B 178 PHE 0.015 0.001 PHE A 223 TRP 0.012 0.001 TRP B 206 HIS 0.011 0.005 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00240 (10880) covalent geometry : angle 0.53635 (14852) hydrogen bonds : bond 0.03638 ( 528) hydrogen bonds : angle 4.89611 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 133 THR cc_start: 0.6611 (m) cc_final: 0.6360 (m) REVERT: B 148 TYR cc_start: 0.8049 (t80) cc_final: 0.7719 (t80) REVERT: B 214 PHE cc_start: 0.8867 (t80) cc_final: 0.8551 (t80) REVERT: B 281 SER cc_start: 0.6911 (t) cc_final: 0.6633 (m) REVERT: C 133 THR cc_start: 0.6635 (m) cc_final: 0.6392 (m) REVERT: C 148 TYR cc_start: 0.8069 (t80) cc_final: 0.7766 (t80) REVERT: C 214 PHE cc_start: 0.9026 (t80) cc_final: 0.8592 (t80) REVERT: C 281 SER cc_start: 0.7081 (t) cc_final: 0.6845 (m) REVERT: C 323 HIS cc_start: 0.5134 (m-70) cc_final: 0.4795 (m-70) REVERT: D 133 THR cc_start: 0.6571 (m) cc_final: 0.6339 (m) REVERT: D 281 SER cc_start: 0.7466 (t) cc_final: 0.7251 (m) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1620 time to fit residues: 71.1276 Evaluate side-chains 273 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN C 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.222834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.187009 restraints weight = 59524.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.192638 restraints weight = 31036.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.196478 restraints weight = 19503.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.198821 restraints weight = 13979.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.200417 restraints weight = 11262.388| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10880 Z= 0.166 Angle : 0.584 4.878 14852 Z= 0.314 Chirality : 0.038 0.131 1784 Planarity : 0.005 0.060 1872 Dihedral : 4.790 18.585 1536 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1412 helix: -0.48 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -1.97 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 220 TYR 0.014 0.002 TYR B 215 PHE 0.019 0.001 PHE A 223 TRP 0.018 0.002 TRP D 167 HIS 0.011 0.005 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00331 (10880) covalent geometry : angle 0.58370 (14852) hydrogen bonds : bond 0.03869 ( 528) hydrogen bonds : angle 5.03565 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2979.62 seconds wall clock time: 51 minutes 30.27 seconds (3090.27 seconds total)