Starting phenix.real_space_refine on Thu Mar 5 09:38:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qcy_4513/03_2026/6qcy_4513.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qcy_4513/03_2026/6qcy_4513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qcy_4513/03_2026/6qcy_4513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qcy_4513/03_2026/6qcy_4513.map" model { file = "/net/cci-nas-00/data/ceres_data/6qcy_4513/03_2026/6qcy_4513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qcy_4513/03_2026/6qcy_4513.cif" } resolution = 4.7 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: 6 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.69, per 1000 atoms: 0.17 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 100.1, 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: 1.89 Conformation dependent library (CDL) restraints added in 577.9 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 12 sheets defined 62.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.740A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.783A pdb=" N ARG A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.222A 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 79 through 92 removed outlier: 3.520A pdb=" N LEU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.624A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.804A pdb=" N ALA A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP A 104 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 149 removed outlier: 4.131A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.963A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.741A pdb=" N LEU B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.783A pdb=" N ARG B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.223A 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 79 through 92 removed outlier: 3.521A pdb=" N LEU B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 3.624A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.803A pdb=" N ALA B 102 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP B 104 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 149 removed outlier: 4.130A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.962A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.739A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 24 " --> pdb=" O PRO C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.783A pdb=" N ARG C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.223A 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 79 through 92 removed outlier: 3.521A pdb=" N LEU C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.624A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.803A pdb=" N ALA C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP C 104 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 149 removed outlier: 4.131A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.963A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'C' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.740A pdb=" N LEU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.783A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.222A 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 79 through 92 removed outlier: 3.521A pdb=" N LEU D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.625A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.803A pdb=" N ALA D 102 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP D 104 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 149 removed outlier: 4.131A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.963A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 273 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 296 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.567A pdb=" N VAL A 311 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR A 310 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 283 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 273 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 296 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 263 removed outlier: 6.566A pdb=" N VAL B 311 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 310 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 283 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 273 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 296 " --> pdb=" O PHE C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 261 through 263 removed outlier: 6.567A pdb=" N VAL C 311 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 310 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 283 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 273 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 296 " --> pdb=" O PHE D 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 261 through 263 removed outlier: 6.567A pdb=" N VAL D 311 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR D 310 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 283 " --> pdb=" O THR D 310 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 11088 1.02 - 1.22: 12 1.22 - 1.42: 4357 1.42 - 1.61: 6447 1.61 - 1.81: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" CA SER D 112 " pdb=" CB SER D 112 " ideal model delta sigma weight residual 1.528 1.464 0.064 2.61e-02 1.47e+03 6.00e+00 bond pdb=" CA SER A 112 " pdb=" CB SER A 112 " ideal model delta sigma weight residual 1.528 1.465 0.063 2.61e-02 1.47e+03 5.92e+00 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.528 1.466 0.063 2.61e-02 1.47e+03 5.78e+00 bond pdb=" CA SER C 112 " pdb=" CB SER C 112 " ideal model delta sigma weight residual 1.528 1.466 0.063 2.61e-02 1.47e+03 5.78e+00 bond pdb=" CB PHE A 214 " pdb=" CG PHE A 214 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.37e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 37041 1.76 - 3.51: 2599 3.51 - 5.27: 232 5.27 - 7.02: 58 7.02 - 8.78: 10 Bond angle restraints: 39940 Sorted by residual: angle pdb=" C LEU C 83 " pdb=" N VAL C 84 " pdb=" CA VAL C 84 " ideal model delta sigma weight residual 120.24 122.39 -2.15 6.30e-01 2.52e+00 1.17e+01 angle pdb=" C LEU B 83 " pdb=" N VAL B 84 " pdb=" CA VAL B 84 " ideal model delta sigma weight residual 120.24 122.36 -2.12 6.30e-01 2.52e+00 1.13e+01 angle pdb=" C LEU A 83 " pdb=" N VAL A 84 " pdb=" CA VAL A 84 " ideal model delta sigma weight residual 120.24 122.35 -2.11 6.30e-01 2.52e+00 1.12e+01 angle pdb=" C LEU D 83 " pdb=" N VAL D 84 " pdb=" CA VAL D 84 " ideal model delta sigma weight residual 120.24 122.34 -2.10 6.30e-01 2.52e+00 1.12e+01 angle pdb=" C SER D 324 " pdb=" N ALA D 325 " pdb=" CA ALA D 325 " ideal model delta sigma weight residual 120.82 125.47 -4.65 1.50e+00 4.44e-01 9.62e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 9233 14.78 - 29.55: 699 29.55 - 44.33: 220 44.33 - 59.10: 120 59.10 - 73.88: 16 Dihedral angle restraints: 10288 sinusoidal: 5604 harmonic: 4684 Sorted by residual: dihedral pdb=" CA ASN C 226 " pdb=" C ASN C 226 " pdb=" N TRP C 227 " pdb=" CA TRP C 227 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASN B 226 " pdb=" C ASN B 226 " pdb=" N TRP B 227 " pdb=" CA TRP B 227 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASN D 226 " pdb=" C ASN D 226 " pdb=" N TRP D 227 " pdb=" CA TRP D 227 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 10285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 906 0.030 - 0.061: 484 0.061 - 0.091: 261 0.091 - 0.121: 105 0.121 - 0.151: 28 Chirality restraints: 1784 Sorted by residual: 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 5.73e-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 5.66e-01 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 5.59e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.014 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" N ALA A 325 " -0.044 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.011 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 49 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C TRP A 49 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 49 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY A 50 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 49 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C TRP D 49 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP D 49 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 50 " -0.013 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.36: 8074 2.36 - 3.05: 63885 3.05 - 3.75: 73394 3.75 - 4.44: 115439 4.44 - 5.14: 173136 Nonbonded interactions: 433928 Sorted by model distance: nonbonded pdb=" O LYS C 74 " pdb=" HE ARG C 110 " model vdw 1.660 2.450 nonbonded pdb=" O LYS B 74 " pdb=" HE ARG B 110 " model vdw 1.660 2.450 nonbonded pdb="HH11 ARG D 120 " pdb=" OE2 GLU D 217 " model vdw 1.660 2.450 nonbonded pdb=" O LYS A 74 " pdb=" HE ARG A 110 " model vdw 1.661 2.450 nonbonded pdb="HH11 ARG C 120 " pdb=" OE2 GLU C 217 " model vdw 1.661 2.450 ... (remaining 433923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 0.030 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.550 Find NCS groups from input model: 0.120 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 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 : 0.009 0.064 10880 Z= 0.446 Angle : 1.045 7.547 14852 Z= 0.586 Chirality : 0.049 0.151 1784 Planarity : 0.007 0.048 1872 Dihedral : 9.698 73.880 3844 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % 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: -4.43 (0.21), residues: 1412 helix: -3.94 (0.14), residues: 612 sheet: -4.03 (0.35), residues: 64 loop : -1.82 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 63 TYR 0.023 0.004 TYR B 178 PHE 0.022 0.004 PHE A 236 TRP 0.014 0.003 TRP D 104 HIS 0.005 0.003 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00921 (10880) covalent geometry : angle 1.04533 (14852) hydrogen bonds : bond 0.32444 ( 480) hydrogen bonds : angle 12.70905 ( 1344) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.140 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: A 1 MET cc_start: -0.2753 (ptm) cc_final: -0.4456 (tpt) REVERT: A 105 LEU cc_start: 0.9215 (mt) cc_final: 0.8890 (mt) REVERT: A 140 LEU cc_start: 0.8556 (tt) cc_final: 0.8248 (tp) REVERT: A 317 VAL cc_start: 0.5246 (t) cc_final: 0.5022 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1445 time to fit residues: 15.4686 Evaluate side-chains 65 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.131 Evaluate side-chains 86 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.127 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: B 1 MET cc_start: -0.2072 (ptm) cc_final: -0.3942 (tpt) REVERT: B 140 LEU cc_start: 0.8621 (tt) cc_final: 0.8327 (tp) REVERT: B 305 GLU cc_start: 0.6327 (mt-10) cc_final: 0.6109 (pt0) REVERT: B 317 VAL cc_start: 0.4907 (t) cc_final: 0.4659 (t) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1288 time to fit residues: 13.2435 Evaluate side-chains 63 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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: 0.0370 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 3.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.209659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.181410 restraints weight = 21604.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.186249 restraints weight = 12251.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.189884 restraints weight = 7830.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192517 restraints weight = 5453.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.193908 restraints weight = 4096.775| |-----------------------------------------------------------------------------| r_work (final): 0.4339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.207998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.180073 restraints weight = 19198.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.185103 restraints weight = 10145.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.188340 restraints weight = 6191.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190833 restraints weight = 4249.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.192239 restraints weight = 3133.883| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.176 Angle : 0.730 7.836 14852 Z= 0.393 Chirality : 0.041 0.149 1784 Planarity : 0.006 0.050 1872 Dihedral : 6.588 24.401 1536 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -4.12 (0.21), residues: 1412 helix: -3.02 (0.15), residues: 704 sheet: -4.09 (0.38), residues: 64 loop : -2.07 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.009 0.002 TYR B 52 PHE 0.021 0.002 PHE D 114 TRP 0.014 0.002 TRP B 167 HIS 0.001 0.000 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00349 (10880) covalent geometry : angle 0.72999 (14852) hydrogen bonds : bond 0.06670 ( 480) hydrogen bonds : angle 7.87211 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.132 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: A 1 MET cc_start: -0.4561 (ptm) cc_final: -0.5209 (tpt) REVERT: A 52 TYR cc_start: 0.8286 (m-10) cc_final: 0.7982 (m-80) REVERT: A 105 LEU cc_start: 0.9269 (mt) cc_final: 0.8962 (mt) REVERT: A 299 MET cc_start: 0.4012 (mtm) cc_final: 0.3804 (ptp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1530 time to fit residues: 15.5279 Evaluate side-chains 65 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.133 Evaluate side-chains 86 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.131 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: B 1 MET cc_start: -0.4320 (ptm) cc_final: -0.5106 (tpt) REVERT: B 105 LEU cc_start: 0.9316 (mt) cc_final: 0.9066 (mt) REVERT: B 305 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5988 (pt0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1545 time to fit residues: 15.4454 Evaluate side-chains 67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 0.0010 chunk 63 optimal weight: 0.0040 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.211988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.182975 restraints weight = 23357.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.187870 restraints weight = 13292.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.191403 restraints weight = 8648.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.193824 restraints weight = 6156.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.195589 restraints weight = 4744.664| |-----------------------------------------------------------------------------| r_work (final): 0.4340 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.209569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.181447 restraints weight = 22258.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.186139 restraints weight = 12534.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.189503 restraints weight = 8142.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.191634 restraints weight = 5802.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.193344 restraints weight = 4507.130| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10880 Z= 0.147 Angle : 0.635 4.986 14852 Z= 0.344 Chirality : 0.039 0.139 1784 Planarity : 0.005 0.040 1872 Dihedral : 5.907 24.208 1536 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.47 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -3.85 (0.21), residues: 1412 helix: -2.54 (0.17), residues: 712 sheet: -4.82 (0.51), residues: 40 loop : -2.32 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 254 TYR 0.010 0.001 TYR A 178 PHE 0.022 0.001 PHE D 114 TRP 0.014 0.002 TRP C 206 HIS 0.003 0.002 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00301 (10880) covalent geometry : angle 0.63457 (14852) hydrogen bonds : bond 0.05205 ( 480) hydrogen bonds : angle 6.94330 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.133 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: A 1 MET cc_start: -0.4637 (ptm) cc_final: -0.5269 (tpt) REVERT: A 105 LEU cc_start: 0.9297 (mt) cc_final: 0.8955 (mt) REVERT: A 275 VAL cc_start: 0.8071 (t) cc_final: 0.7701 (m) REVERT: A 299 MET cc_start: 0.3910 (mtm) cc_final: 0.3201 (ptp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1500 time to fit residues: 14.5358 Evaluate side-chains 73 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.151 Evaluate side-chains 79 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.130 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: B 1 MET cc_start: -0.4273 (ptm) cc_final: -0.5206 (tpt) REVERT: B 83 LEU cc_start: 0.9084 (mt) cc_final: 0.8862 (mt) REVERT: B 105 LEU cc_start: 0.9288 (mt) cc_final: 0.8940 (mt) REVERT: B 246 GLU cc_start: 0.8440 (pt0) cc_final: 0.8051 (pt0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1538 time to fit residues: 14.1934 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 0.0050 chunk 99 optimal weight: 30.0000 chunk 103 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 overall best weight: 5.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.210254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.181233 restraints weight = 23300.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.185976 restraints weight = 13428.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.189237 restraints weight = 8844.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.191762 restraints weight = 6391.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193575 restraints weight = 4895.091| |-----------------------------------------------------------------------------| r_work (final): 0.4312 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.208575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180608 restraints weight = 24046.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.185493 restraints weight = 13618.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.189044 restraints weight = 8803.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191388 restraints weight = 6211.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.193159 restraints weight = 4749.344| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10880 Z= 0.192 Angle : 0.648 6.440 14852 Z= 0.354 Chirality : 0.040 0.132 1784 Planarity : 0.006 0.054 1872 Dihedral : 5.786 23.779 1536 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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 (0.22), residues: 1412 helix: -2.16 (0.18), residues: 692 sheet: -4.76 (0.53), residues: 40 loop : -2.14 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 254 TYR 0.028 0.002 TYR D 215 PHE 0.023 0.002 PHE D 114 TRP 0.020 0.002 TRP D 206 HIS 0.002 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00394 (10880) covalent geometry : angle 0.64815 (14852) hydrogen bonds : bond 0.04637 ( 480) hydrogen bonds : angle 6.67326 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.137 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: A 1 MET cc_start: -0.4487 (ptm) cc_final: -0.5004 (tpt) REVERT: A 83 LEU cc_start: 0.9106 (mt) cc_final: 0.8905 (mt) REVERT: A 105 LEU cc_start: 0.9296 (mt) cc_final: 0.8924 (mt) REVERT: A 217 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7564 (mm-30) REVERT: A 218 VAL cc_start: 0.8324 (t) cc_final: 0.7481 (t) REVERT: A 275 VAL cc_start: 0.8277 (t) cc_final: 0.7957 (m) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1355 time to fit residues: 12.2851 Evaluate side-chains 66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.128 Evaluate side-chains 75 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.126 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: B 1 MET cc_start: -0.4268 (ptm) cc_final: -0.5279 (tpt) REVERT: B 83 LEU cc_start: 0.9164 (mt) cc_final: 0.8946 (mt) REVERT: B 105 LEU cc_start: 0.9252 (mt) cc_final: 0.8887 (mt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1403 time to fit residues: 12.4667 Evaluate side-chains 61 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 0.0670 chunk 120 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.212826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.183467 restraints weight = 22404.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.188582 restraints weight = 12609.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192316 restraints weight = 8138.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.195090 restraints weight = 5734.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.196827 restraints weight = 4312.256| |-----------------------------------------------------------------------------| r_work (final): 0.4350 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.210995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.181687 restraints weight = 22988.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.186690 restraints weight = 13002.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.190372 restraints weight = 8476.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.192849 restraints weight = 6013.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.194689 restraints weight = 4615.745| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10880 Z= 0.118 Angle : 0.559 4.759 14852 Z= 0.298 Chirality : 0.038 0.128 1784 Planarity : 0.005 0.047 1872 Dihedral : 5.342 22.262 1536 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % 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: -3.17 (0.22), residues: 1412 helix: -1.98 (0.18), residues: 676 sheet: -4.59 (0.51), residues: 40 loop : -2.01 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.005 0.001 TYR C 10 PHE 0.017 0.001 PHE C 114 TRP 0.015 0.001 TRP B 206 HIS 0.002 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00254 (10880) covalent geometry : angle 0.55926 (14852) hydrogen bonds : bond 0.03906 ( 480) hydrogen bonds : angle 6.14857 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.4430 (ptm) cc_final: -0.5041 (tpt) REVERT: A 83 LEU cc_start: 0.9133 (mt) cc_final: 0.8893 (mt) REVERT: A 105 LEU cc_start: 0.9322 (mt) cc_final: 0.8933 (mt) REVERT: A 217 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7726 (mm-30) REVERT: A 218 VAL cc_start: 0.8269 (t) cc_final: 0.7560 (t) REVERT: A 246 GLU cc_start: 0.8382 (pt0) cc_final: 0.8169 (mp0) REVERT: A 275 VAL cc_start: 0.8291 (t) cc_final: 0.8008 (m) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1252 time to fit residues: 11.3697 Evaluate side-chains 66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.138 Evaluate side-chains 77 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.137 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: B 1 MET cc_start: -0.4374 (ptm) cc_final: -0.5382 (tpt) REVERT: B 83 LEU cc_start: 0.9117 (mt) cc_final: 0.8880 (mt) REVERT: B 105 LEU cc_start: 0.9365 (mt) cc_final: 0.8996 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1221 time to fit residues: 11.3157 Evaluate side-chains 61 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.211879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.183171 restraints weight = 22320.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.188242 restraints weight = 12876.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.191919 restraints weight = 8373.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.194396 restraints weight = 5912.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.196180 restraints weight = 4522.431| |-----------------------------------------------------------------------------| r_work (final): 0.4357 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.209903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.180507 restraints weight = 22897.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.185328 restraints weight = 13052.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188767 restraints weight = 8487.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.190989 restraints weight = 6069.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.192636 restraints weight = 4723.535| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.5343 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= 0.118 Angle : 0.541 4.754 14852 Z= 0.289 Chirality : 0.037 0.115 1784 Planarity : 0.005 0.048 1872 Dihedral : 5.006 21.124 1536 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.95 (0.22), residues: 1412 helix: -1.74 (0.18), residues: 704 sheet: -4.29 (0.52), residues: 40 loop : -1.95 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 254 TYR 0.008 0.001 TYR A 215 PHE 0.018 0.001 PHE A 214 TRP 0.019 0.001 TRP B 206 HIS 0.002 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00253 (10880) covalent geometry : angle 0.54058 (14852) hydrogen bonds : bond 0.03513 ( 480) hydrogen bonds : angle 5.78085 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.128 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: A 1 MET cc_start: -0.4395 (ptm) cc_final: -0.5089 (tpt) REVERT: A 83 LEU cc_start: 0.9079 (mt) cc_final: 0.8843 (mt) REVERT: A 105 LEU cc_start: 0.9269 (mt) cc_final: 0.8850 (mt) REVERT: A 217 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7682 (mm-30) REVERT: A 218 VAL cc_start: 0.8160 (t) cc_final: 0.7530 (t) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1086 time to fit residues: 10.1966 Evaluate side-chains 71 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.128 Evaluate side-chains 72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.129 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: B 1 MET cc_start: -0.3575 (ptm) cc_final: -0.4752 (tpt) REVERT: B 83 LEU cc_start: 0.9055 (mt) cc_final: 0.8829 (mt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1345 time to fit residues: 11.4996 Evaluate side-chains 61 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 0.0970 chunk 105 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.208843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180449 restraints weight = 19758.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.185490 restraints weight = 10700.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.189176 restraints weight = 6721.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191798 restraints weight = 4637.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.193561 restraints weight = 3428.115| |-----------------------------------------------------------------------------| r_work (final): 0.4360 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.210007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.180470 restraints weight = 22653.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185361 restraints weight = 13001.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.189007 restraints weight = 8470.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.191334 restraints weight = 6022.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.193311 restraints weight = 4671.312| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10880 Z= 0.125 Angle : 0.554 4.910 14852 Z= 0.294 Chirality : 0.038 0.123 1784 Planarity : 0.005 0.042 1872 Dihedral : 5.010 21.786 1536 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.83 (0.22), residues: 1412 helix: -1.57 (0.19), residues: 704 sheet: -4.11 (0.54), residues: 40 loop : -1.99 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.006 0.001 TYR A 178 PHE 0.016 0.001 PHE D 114 TRP 0.018 0.001 TRP B 206 HIS 0.001 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00277 (10880) covalent geometry : angle 0.55351 (14852) hydrogen bonds : bond 0.03437 ( 480) hydrogen bonds : angle 5.65125 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.133 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: C 1 MET cc_start: -0.3752 (ptm) cc_final: -0.4795 (tpt) REVERT: C 83 LEU cc_start: 0.8988 (mt) cc_final: 0.8762 (mt) REVERT: C 217 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7509 (mm-30) REVERT: C 218 VAL cc_start: 0.8254 (t) cc_final: 0.7634 (t) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1286 time to fit residues: 11.4260 Evaluate side-chains 59 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.131 Evaluate side-chains 76 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.131 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: B 1 MET cc_start: -0.3550 (ptm) cc_final: -0.4723 (tpt) REVERT: B 83 LEU cc_start: 0.9095 (mt) cc_final: 0.8859 (mt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1588 time to fit residues: 14.0138 Evaluate side-chains 70 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 chunk 45 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 0.0370 chunk 122 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.211554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183274 restraints weight = 21341.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188282 restraints weight = 12392.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.192089 restraints weight = 8090.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.194549 restraints weight = 5725.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.196690 restraints weight = 4403.385| |-----------------------------------------------------------------------------| r_work (final): 0.4376 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.212629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183339 restraints weight = 22298.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.188298 restraints weight = 12751.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.192053 restraints weight = 8286.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.194826 restraints weight = 5873.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.196772 restraints weight = 4449.417| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10880 Z= 0.109 Angle : 0.569 9.050 14852 Z= 0.295 Chirality : 0.038 0.115 1784 Planarity : 0.007 0.130 1872 Dihedral : 4.805 21.608 1536 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.88 (0.21), residues: 1412 helix: -1.55 (0.18), residues: 688 sheet: -3.81 (0.51), residues: 40 loop : -2.13 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 254 TYR 0.005 0.001 TYR B 10 PHE 0.014 0.001 PHE D 114 TRP 0.021 0.001 TRP B 206 HIS 0.002 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00251 (10880) covalent geometry : angle 0.56913 (14852) hydrogen bonds : bond 0.03078 ( 480) hydrogen bonds : angle 5.43792 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.129 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: C 1 MET cc_start: -0.4316 (ptm) cc_final: -0.4955 (tpt) REVERT: C 83 LEU cc_start: 0.8951 (mt) cc_final: 0.8747 (mt) REVERT: C 105 LEU cc_start: 0.9322 (mt) cc_final: 0.8886 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0959 time to fit residues: 8.9767 Evaluate side-chains 59 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.131 Evaluate side-chains 78 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.137 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: B 1 MET cc_start: -0.4113 (ptm) cc_final: -0.5281 (tpt) REVERT: B 83 LEU cc_start: 0.9128 (mt) cc_final: 0.8879 (mt) REVERT: B 272 MET cc_start: 0.6218 (tmm) cc_final: 0.5977 (tmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1601 time to fit residues: 14.5228 Evaluate side-chains 69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 58 optimal weight: 0.0980 chunk 36 optimal weight: 7.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.210307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.180527 restraints weight = 21938.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.185465 restraints weight = 12557.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.189075 restraints weight = 8165.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.191777 restraints weight = 5779.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.193361 restraints weight = 4366.277| |-----------------------------------------------------------------------------| r_work (final): 0.4319 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.209234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.180590 restraints weight = 21619.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.185181 restraints weight = 12804.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.188443 restraints weight = 8477.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190588 restraints weight = 6154.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.192186 restraints weight = 4831.392| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10880 Z= 0.163 Angle : 0.604 7.396 14852 Z= 0.324 Chirality : 0.039 0.136 1784 Planarity : 0.005 0.076 1872 Dihedral : 4.833 19.891 1536 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.87 (0.22), residues: 1412 helix: -1.56 (0.19), residues: 704 sheet: -3.96 (0.52), residues: 40 loop : -2.08 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 249 TYR 0.012 0.001 TYR A 178 PHE 0.020 0.001 PHE B 114 TRP 0.019 0.002 TRP B 206 HIS 0.004 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00333 (10880) covalent geometry : angle 0.60448 (14852) hydrogen bonds : bond 0.03233 ( 480) hydrogen bonds : angle 5.49865 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.132 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: C 83 LEU cc_start: 0.9098 (mt) cc_final: 0.8857 (mt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1119 time to fit residues: 9.9561 Evaluate side-chains 66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.130 Evaluate side-chains 77 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.130 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: B 1 MET cc_start: -0.5422 (ptm) cc_final: -0.5635 (tpt) REVERT: B 83 LEU cc_start: 0.9098 (mt) cc_final: 0.8859 (mt) REVERT: B 197 MET cc_start: 0.7799 (tpt) cc_final: 0.7324 (tpp) REVERT: B 272 MET cc_start: 0.6289 (tmm) cc_final: 0.6043 (tmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1586 time to fit residues: 14.1724 Evaluate side-chains 69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 overall best weight: 6.1388 ------------------------------------------------------------------------------- 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 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.207791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180002 restraints weight = 22024.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.184608 restraints weight = 12925.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.187889 restraints weight = 8569.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190410 restraints weight = 6212.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.191983 restraints weight = 4765.461| |-----------------------------------------------------------------------------| r_work (final): 0.4328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.208128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178933 restraints weight = 23435.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.183669 restraints weight = 13361.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.186919 restraints weight = 8719.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.189426 restraints weight = 6303.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.190941 restraints weight = 4820.112| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10880 Z= 0.201 Angle : 0.672 6.099 14852 Z= 0.363 Chirality : 0.040 0.121 1784 Planarity : 0.008 0.184 1872 Dihedral : 5.159 28.119 1536 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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: -3.30 (0.21), residues: 1412 helix: -1.91 (0.18), residues: 704 sheet: -3.85 (0.54), residues: 40 loop : -2.34 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 120 TYR 0.024 0.002 TYR D 215 PHE 0.018 0.002 PHE B 114 TRP 0.024 0.002 TRP B 206 HIS 0.006 0.004 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00410 (10880) covalent geometry : angle 0.67223 (14852) hydrogen bonds : bond 0.03507 ( 480) hydrogen bonds : angle 5.68480 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.130 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: C 83 LEU cc_start: 0.9031 (mt) cc_final: 0.8823 (mt) REVERT: C 197 MET cc_start: 0.7615 (tpt) cc_final: 0.7271 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1132 time to fit residues: 9.8833 Evaluate side-chains 65 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.135 Evaluate side-chains 76 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.130 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: B 83 LEU cc_start: 0.9156 (mt) cc_final: 0.8921 (mt) REVERT: B 272 MET cc_start: 0.6286 (tmm) cc_final: 0.6028 (tmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1135 time to fit residues: 10.5784 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 122 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 0.0010 chunk 23 optimal weight: 0.6980 chunk 131 optimal weight: 0.0970 overall best weight: 0.1962 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.207821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.180506 restraints weight = 19022.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.185272 restraints weight = 10706.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.188543 restraints weight = 6892.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.191113 restraints weight = 4900.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.192734 restraints weight = 3681.236| |-----------------------------------------------------------------------------| r_work (final): 0.4395 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.212362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182953 restraints weight = 22497.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.188095 restraints weight = 13124.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.191914 restraints weight = 8563.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.194555 restraints weight = 6052.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.196076 restraints weight = 4616.983| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10880 Z= 0.108 Angle : 0.571 5.505 14852 Z= 0.295 Chirality : 0.038 0.115 1784 Planarity : 0.006 0.142 1872 Dihedral : 4.743 20.998 1536 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % 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: -2.90 (0.21), residues: 1412 helix: -1.57 (0.18), residues: 704 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 120 TYR 0.005 0.001 TYR D 148 PHE 0.013 0.001 PHE D 114 TRP 0.022 0.001 TRP B 206 HIS 0.006 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00238 (10880) covalent geometry : angle 0.57050 (14852) hydrogen bonds : bond 0.02911 ( 480) hydrogen bonds : angle 5.31378 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.58 seconds wall clock time: 37 minutes 1.72 seconds (2221.72 seconds total)