Starting phenix.real_space_refine on Sun Sep 13 05:38:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qcy_4513/09_2026/6qcy_4513.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qcy_4513/09_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_4513/09_2026/6qcy_4513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qcy_4513/09_2026/6qcy_4513.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qcy_4513/09_2026/6qcy_4513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qcy_4513/09_2026/6qcy_4513.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qcy_4513/09_2026/6qcy_4513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qcy_4513/09_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-2.2.1-6174/lib/python3.11/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: 4.22, per 1000 atoms: 0.19 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: 2.33 Conformation dependent library (CDL) restraints added in 760.9 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: 0.54 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: 5.17 Time building geometry restraints manager: 3.17 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: 0.070 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 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/Z covalent geometry : bond 0.00921 / 0.45 (10880) covalent geometry : angle 1.04533 / 0.59 (14852) hydrogen bonds : bond 0.32444 / 21.69 ( 480) hydrogen bonds : angle 12.70905 / 9.14 ( 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 : 0.138 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: 0.1292 time to fit residues: 14.1073 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 86 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.086 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: 0.1214 time to fit residues: 12.5620 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 : 0.148 ------------------------------------------------------------------------------- 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... A 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.209740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.181125 restraints weight = 21590.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.186041 restraints weight = 12118.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.189735 restraints weight = 7743.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.192182 restraints weight = 5398.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.193941 restraints weight = 4095.709| |-----------------------------------------------------------------------------| r_work (final): 0.4338 |-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: 0.6219 moved from start: 0.2813 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 : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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/Z covalent geometry : bond 0.00349 / 0.18 (10880) covalent geometry : angle 0.72999 / 0.39 (14852) hydrogen bonds : bond 0.06670 / 4.43 ( 480) hydrogen bonds : angle 7.87211 / 5.62 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.137 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: A 1 MET cc_start: -0.4555 (ptm) cc_final: -0.5205 (tpt) REVERT: A 52 TYR cc_start: 0.8284 (m-10) cc_final: 0.7980 (m-80) REVERT: A 105 LEU cc_start: 0.9271 (mt) cc_final: 0.8965 (mt) REVERT: A 299 MET cc_start: 0.4009 (mtm) cc_final: 0.3802 (ptp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1419 time to fit residues: 14.6455 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 : 0.140 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 : 0.135 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: -0.4320 (ptm) cc_final: -0.5107 (tpt) REVERT: B 105 LEU cc_start: 0.9316 (mt) cc_final: 0.9062 (mt) REVERT: B 305 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5947 (pt0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1401 time to fit residues: 14.3394 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 : 0.134 ------------------------------------------------------------------------------- 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: 0.0980 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN A 216 GLN A 226 ASN B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.211656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182249 restraints weight = 23202.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.187174 restraints weight = 13114.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.190676 restraints weight = 8553.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193269 restraints weight = 6105.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.195150 restraints weight = 4666.953| |-----------------------------------------------------------------------------| r_work (final): 0.4316 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.208397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.180656 restraints weight = 20784.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.185347 restraints weight = 11640.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188713 restraints weight = 7507.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190880 restraints weight = 5314.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.192616 restraints weight = 4097.753| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10880 Z= 0.166 Angle : 0.658 5.309 14852 Z= 0.359 Chirality : 0.040 0.144 1784 Planarity : 0.006 0.041 1872 Dihedral : 6.112 23.789 1536 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % 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: -3.87 (0.21), residues: 1412 helix: -2.58 (0.16), residues: 736 sheet: -4.88 (0.48), residues: 40 loop : -2.24 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.011 0.002 TYR A 178 PHE 0.021 0.001 PHE D 114 TRP 0.016 0.002 TRP A 206 HIS 0.003 0.002 HIS D 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (10880) covalent geometry : angle 0.65779 / 0.36 (14852) hydrogen bonds : bond 0.05571 / 3.65 ( 480) hydrogen bonds : angle 7.17668 / 5.12 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.162 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: -0.4743 (ptm) cc_final: -0.5373 (tpt) REVERT: A 83 LEU cc_start: 0.9164 (mt) cc_final: 0.8961 (mt) REVERT: A 105 LEU cc_start: 0.9294 (mt) cc_final: 0.8956 (mt) REVERT: A 299 MET cc_start: 0.3747 (mtm) cc_final: 0.3292 (ptp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1278 time to fit residues: 12.5100 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 : 0.143 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 : 0.140 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: B 1 MET cc_start: -0.4182 (ptm) cc_final: -0.5010 (tpt) REVERT: B 105 LEU cc_start: 0.9284 (mt) cc_final: 0.8938 (mt) REVERT: B 305 GLU cc_start: 0.6385 (mt-10) cc_final: 0.6005 (pt0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1321 time to fit residues: 12.3314 Evaluate side-chains 62 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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: 9.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 89 optimal weight: 0.0970 chunk 68 optimal weight: 0.0470 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 40.0000 chunk 31 optimal weight: 0.0570 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.213115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.183495 restraints weight = 21355.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188511 restraints weight = 12288.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.191977 restraints weight = 8041.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.194585 restraints weight = 5796.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.196432 restraints weight = 4437.201| |-----------------------------------------------------------------------------| r_work (final): 0.4400 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.210956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183078 restraints weight = 21423.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.188094 restraints weight = 12145.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191703 restraints weight = 7916.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.194005 restraints weight = 5667.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.196209 restraints weight = 4408.160| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10880 Z= 0.133 Angle : 0.586 4.945 14852 Z= 0.310 Chirality : 0.039 0.131 1784 Planarity : 0.005 0.059 1872 Dihedral : 5.444 23.082 1536 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -3.16 (0.21), residues: 1412 helix: -1.91 (0.18), residues: 684 sheet: -4.76 (0.50), residues: 40 loop : -2.04 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 254 TYR 0.011 0.001 TYR A 52 PHE 0.017 0.001 PHE D 114 TRP 0.027 0.002 TRP A 206 HIS 0.001 0.000 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10880) covalent geometry : angle 0.58603 / 0.31 (14852) hydrogen bonds : bond 0.04361 / 2.85 ( 480) hydrogen bonds : angle 6.39213 / 4.57 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.145 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: -0.4473 (ptm) cc_final: -0.5336 (tpt) REVERT: A 56 LEU cc_start: 0.9491 (tp) cc_final: 0.9288 (tp) REVERT: A 105 LEU cc_start: 0.9347 (mt) cc_final: 0.8960 (mt) REVERT: A 217 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7605 (mm-30) REVERT: A 218 VAL cc_start: 0.8242 (t) cc_final: 0.7489 (t) REVERT: A 275 VAL cc_start: 0.8154 (t) cc_final: 0.7839 (m) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1345 time to fit residues: 12.8484 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 : 0.136 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 : 0.144 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: B 1 MET cc_start: -0.4193 (ptm) cc_final: -0.5073 (tpt) REVERT: B 105 LEU cc_start: 0.9357 (mt) cc_final: 0.8994 (mt) REVERT: B 217 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7521 (mm-30) REVERT: B 218 VAL cc_start: 0.8172 (t) cc_final: 0.7452 (t) REVERT: B 275 VAL cc_start: 0.8457 (t) cc_final: 0.8155 (m) REVERT: B 305 GLU cc_start: 0.6310 (mt-10) cc_final: 0.5926 (pt0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1187 time to fit residues: 10.5774 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 : 0.144 ------------------------------------------------------------------------------- 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: 0.0270 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 0.0050 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 overall best weight: 0.2852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.213659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.183509 restraints weight = 22427.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188782 restraints weight = 12708.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.192648 restraints weight = 8168.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.195141 restraints weight = 5727.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.197068 restraints weight = 4396.774| |-----------------------------------------------------------------------------| r_work (final): 0.4365 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.214332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.185700 restraints weight = 22009.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.190979 restraints weight = 12574.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194741 restraints weight = 8190.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.197276 restraints weight = 5776.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.199402 restraints weight = 4424.136| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10880 Z= 0.115 Angle : 0.555 5.031 14852 Z= 0.296 Chirality : 0.038 0.133 1784 Planarity : 0.005 0.057 1872 Dihedral : 5.276 22.999 1536 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.68 (0.19), residues: 688 sheet: -4.67 (0.48), residues: 40 loop : -2.01 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 127 TYR 0.021 0.002 TYR A 215 PHE 0.042 0.001 PHE C 214 TRP 0.015 0.001 TRP C 206 HIS 0.001 0.000 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (10880) covalent geometry : angle 0.55509 / 0.30 (14852) hydrogen bonds : bond 0.04082 / 2.67 ( 480) hydrogen bonds : angle 6.09102 / 4.36 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.149 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: -0.4203 (ptm) cc_final: -0.5061 (tpt) REVERT: C 83 LEU cc_start: 0.8994 (mt) cc_final: 0.8786 (mt) REVERT: C 105 LEU cc_start: 0.9397 (mt) cc_final: 0.8977 (mt) REVERT: C 217 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7392 (mm-30) REVERT: C 218 VAL cc_start: 0.8119 (t) cc_final: 0.7298 (t) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0908 time to fit residues: 8.5791 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 : 0.122 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 : 0.136 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: B 1 MET cc_start: -0.4125 (ptm) cc_final: -0.5175 (tpt) REVERT: B 83 LEU cc_start: 0.8963 (mt) cc_final: 0.8761 (mt) REVERT: B 101 CYS cc_start: 0.7732 (m) cc_final: 0.7517 (m) REVERT: B 105 LEU cc_start: 0.9351 (mt) cc_final: 0.8937 (mt) REVERT: B 217 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7437 (mm-30) REVERT: B 218 VAL cc_start: 0.8262 (t) cc_final: 0.7536 (t) REVERT: B 305 GLU cc_start: 0.6285 (mt-10) cc_final: 0.5896 (pt0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1033 time to fit residues: 9.4178 Evaluate side-chains 64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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: 5.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 124 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 ASN B 216 GLN B 226 ASN C 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.209819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.181192 restraints weight = 21929.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.186252 restraints weight = 12711.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.190014 restraints weight = 8215.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.192412 restraints weight = 5797.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.194299 restraints weight = 4464.007| |-----------------------------------------------------------------------------| r_work (final): 0.4342 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.210536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.182880 restraints weight = 22685.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.187670 restraints weight = 13116.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.191220 restraints weight = 8555.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193450 restraints weight = 6046.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.195364 restraints weight = 4694.751| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10880 Z= 0.129 Angle : 0.553 4.758 14852 Z= 0.297 Chirality : 0.038 0.125 1784 Planarity : 0.005 0.045 1872 Dihedral : 5.054 22.092 1536 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % 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: -2.44 (0.23), residues: 1412 helix: -1.27 (0.20), residues: 696 sheet: -4.27 (0.51), residues: 40 loop : -1.75 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 220 TYR 0.006 0.001 TYR D 215 PHE 0.018 0.001 PHE B 214 TRP 0.017 0.001 TRP C 206 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (10880) covalent geometry : angle 0.55292 / 0.30 (14852) hydrogen bonds : bond 0.03727 / 2.47 ( 480) hydrogen bonds : angle 5.73193 / 4.15 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.138 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: C 1 MET cc_start: -0.4140 (ptm) cc_final: -0.5185 (tpt) REVERT: C 83 LEU cc_start: 0.9067 (mt) cc_final: 0.8854 (mt) REVERT: C 105 LEU cc_start: 0.9400 (mt) cc_final: 0.9034 (mt) REVERT: C 197 MET cc_start: 0.7695 (tpp) cc_final: 0.7401 (tpp) REVERT: C 217 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7514 (mm-30) REVERT: C 218 VAL cc_start: 0.8246 (t) cc_final: 0.7487 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1023 time to fit residues: 9.9410 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 : 0.135 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 : 0.133 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: B 1 MET cc_start: -0.3556 (ptm) cc_final: -0.4710 (tpt) REVERT: B 83 LEU cc_start: 0.9130 (mt) cc_final: 0.8901 (mt) REVERT: B 105 LEU cc_start: 0.9381 (mt) cc_final: 0.9007 (mt) REVERT: B 217 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7515 (mm-30) REVERT: B 218 VAL cc_start: 0.8238 (t) cc_final: 0.7481 (t) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1104 time to fit residues: 9.6534 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 : 0.139 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 9.9990 chunk 107 optimal weight: 0.0770 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 95 optimal weight: 40.0000 chunk 130 optimal weight: 10.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.208963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180319 restraints weight = 22737.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.185379 restraints weight = 12947.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.189116 restraints weight = 8413.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.191593 restraints weight = 5937.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.193459 restraints weight = 4537.321| |-----------------------------------------------------------------------------| r_work (final): 0.4315 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.206730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180067 restraints weight = 20664.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.184719 restraints weight = 11520.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.187887 restraints weight = 7356.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.190257 restraints weight = 5213.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.191858 restraints weight = 3979.303| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10880 Z= 0.171 Angle : 0.614 4.705 14852 Z= 0.331 Chirality : 0.039 0.145 1784 Planarity : 0.005 0.044 1872 Dihedral : 5.082 21.447 1536 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.31 (0.23), residues: 1412 helix: -1.14 (0.19), residues: 700 sheet: -3.99 (0.50), residues: 40 loop : -1.72 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 127 TYR 0.015 0.002 TYR D 178 PHE 0.016 0.002 PHE B 114 TRP 0.018 0.002 TRP C 206 HIS 0.003 0.002 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (10880) covalent geometry : angle 0.61364 / 0.33 (14852) hydrogen bonds : bond 0.03507 / 2.34 ( 480) hydrogen bonds : angle 5.63366 / 4.09 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.138 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: -0.4288 (ptm) cc_final: -0.5127 (tpt) REVERT: C 83 LEU cc_start: 0.9104 (mt) cc_final: 0.8878 (mt) REVERT: C 197 MET cc_start: 0.7863 (tpp) cc_final: 0.7288 (tpt) REVERT: C 217 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7658 (mm-30) REVERT: C 218 VAL cc_start: 0.8166 (t) cc_final: 0.7544 (t) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1060 time to fit residues: 9.6483 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 : 0.142 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 : 0.149 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: D 1 MET cc_start: -0.3451 (ptm) cc_final: -0.4609 (tpt) REVERT: D 83 LEU cc_start: 0.9050 (mt) cc_final: 0.8843 (mt) REVERT: D 217 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7852 (mm-30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1235 time to fit residues: 11.0923 Evaluate side-chains 64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 20.0000 chunk 44 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 0.0870 chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 226 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.210806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.181347 restraints weight = 22255.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.186559 restraints weight = 12865.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.190316 restraints weight = 8349.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.192687 restraints weight = 5902.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.194694 restraints weight = 4547.399| |-----------------------------------------------------------------------------| r_work (final): 0.4301 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.208961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.181846 restraints weight = 20413.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.186766 restraints weight = 11386.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.190263 restraints weight = 7303.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.192804 restraints weight = 5147.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.194537 restraints weight = 3867.267| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10880 Z= 0.125 Angle : 0.565 4.749 14852 Z= 0.298 Chirality : 0.038 0.120 1784 Planarity : 0.006 0.110 1872 Dihedral : 4.992 21.609 1536 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % 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: -2.14 (0.23), residues: 1412 helix: -0.96 (0.20), residues: 704 sheet: -3.29 (0.57), residues: 40 loop : -1.73 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 254 TYR 0.007 0.001 TYR C 178 PHE 0.018 0.001 PHE B 114 TRP 0.016 0.001 TRP C 206 HIS 0.002 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10880) covalent geometry : angle 0.56476 / 0.30 (14852) hydrogen bonds : bond 0.03373 / 2.27 ( 480) hydrogen bonds : angle 5.47804 / 3.98 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.157 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: -0.4156 (ptm) cc_final: -0.5075 (tpt) REVERT: C 83 LEU cc_start: 0.9069 (mt) cc_final: 0.8850 (mt) REVERT: C 197 MET cc_start: 0.8122 (tpp) cc_final: 0.7854 (tpt) REVERT: C 217 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7689 (mm-30) REVERT: C 218 VAL cc_start: 0.8145 (t) cc_final: 0.7552 (t) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0879 time to fit residues: 8.2378 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 : 0.141 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 : 0.134 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: -0.3559 (ptm) cc_final: -0.4623 (tpt) REVERT: B 83 LEU cc_start: 0.9096 (mt) cc_final: 0.8871 (mt) REVERT: B 217 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7682 (mm-30) REVERT: B 218 VAL cc_start: 0.8159 (t) cc_final: 0.7589 (t) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1198 time to fit residues: 10.6536 Evaluate side-chains 64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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: 9.9990 chunk 102 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 61 optimal weight: 0.0470 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4553 r_free = 0.4553 target = 0.209716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180329 restraints weight = 21795.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.185363 restraints weight = 12992.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.189023 restraints weight = 8589.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.192099 restraints weight = 6180.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193992 restraints weight = 4621.446| |-----------------------------------------------------------------------------| r_work (final): 0.4400 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.209422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.183270 restraints weight = 19651.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.187859 restraints weight = 11400.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.191259 restraints weight = 7484.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193820 restraints weight = 5335.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.195365 restraints weight = 4058.848| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10880 Z= 0.108 Angle : 0.541 4.803 14852 Z= 0.286 Chirality : 0.038 0.119 1784 Planarity : 0.005 0.069 1872 Dihedral : 4.825 21.184 1536 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.23), residues: 1412 helix: -0.75 (0.20), residues: 704 sheet: -2.56 (0.45), residues: 72 loop : -1.57 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 254 TYR 0.006 0.001 TYR B 52 PHE 0.014 0.001 PHE D 114 TRP 0.015 0.001 TRP A 206 HIS 0.003 0.002 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10880) covalent geometry : angle 0.54107 / 0.29 (14852) hydrogen bonds : bond 0.03113 / 2.08 ( 480) hydrogen bonds : angle 5.35555 / 3.89 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.144 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 1 MET cc_start: -0.3759 (ptm) cc_final: -0.4790 (tpt) REVERT: C 56 LEU cc_start: 0.9501 (tp) cc_final: 0.9301 (tp) REVERT: C 217 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7615 (mm-30) REVERT: C 218 VAL cc_start: 0.8096 (t) cc_final: 0.7568 (t) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0909 time to fit residues: 8.6953 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 : 0.144 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 : 0.108 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: D 1 MET cc_start: -0.4028 (ptm) cc_final: -0.5036 (tpt) REVERT: D 164 GLN cc_start: 0.6188 (pm20) cc_final: 0.5900 (pm20) REVERT: D 217 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7757 (mm-30) REVERT: D 218 VAL cc_start: 0.8124 (t) cc_final: 0.7562 (t) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0966 time to fit residues: 8.6797 Evaluate side-chains 64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.4554 r_free = 0.4554 target = 0.209315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180772 restraints weight = 22134.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.185712 restraints weight = 13256.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.189344 restraints weight = 8723.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192200 restraints weight = 6245.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.194044 restraints weight = 4713.809| |-----------------------------------------------------------------------------| r_work (final): 0.4383 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.209024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.182462 restraints weight = 21498.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.187350 restraints weight = 12171.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.190565 restraints weight = 7792.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.193328 restraints weight = 5564.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194599 restraints weight = 4171.471| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10880 Z= 0.111 Angle : 0.548 5.387 14852 Z= 0.288 Chirality : 0.038 0.115 1784 Planarity : 0.005 0.046 1872 Dihedral : 4.663 20.438 1536 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.23), residues: 1412 helix: -0.62 (0.20), residues: 708 sheet: -2.42 (0.47), residues: 72 loop : -1.55 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 127 TYR 0.007 0.001 TYR B 178 PHE 0.015 0.001 PHE B 114 TRP 0.023 0.001 TRP B 206 HIS 0.003 0.002 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10880) covalent geometry : angle 0.54780 / 0.29 (14852) hydrogen bonds : bond 0.02968 / 1.97 ( 480) hydrogen bonds : angle 5.23228 / 3.80 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.137 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: C 1 MET cc_start: -0.3540 (ptm) cc_final: -0.4570 (tpt) REVERT: C 197 MET cc_start: 0.7749 (tpt) cc_final: 0.7202 (tpp) REVERT: C 198 SER cc_start: 0.8557 (m) cc_final: 0.8018 (p) REVERT: C 217 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7543 (mm-30) REVERT: C 218 VAL cc_start: 0.8134 (t) cc_final: 0.7702 (t) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1026 time to fit residues: 9.6117 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 : 0.141 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 : 0.138 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: D 1 MET cc_start: -0.3764 (ptm) cc_final: -0.4796 (tpt) REVERT: D 217 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7717 (mm-30) REVERT: D 218 VAL cc_start: 0.8102 (t) cc_final: 0.7570 (t) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1166 time to fit residues: 10.5413 Evaluate side-chains 57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.081 ------------------------------------------------------------------------------- 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: 8.9990 chunk 109 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 chunk 131 optimal weight: 0.0470 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 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 = 0.4558 r_free = 0.4558 target = 0.210758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181997 restraints weight = 22792.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.187119 restraints weight = 13728.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.191139 restraints weight = 9109.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193680 restraints weight = 6477.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.195743 restraints weight = 4960.472| |-----------------------------------------------------------------------------| r_work (final): 0.4322 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.210956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.183723 restraints weight = 21812.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.188785 restraints weight = 12437.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.192194 restraints weight = 8014.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194282 restraints weight = 5687.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.196106 restraints weight = 4445.741| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10880 Z= 0.126 Angle : 0.580 8.415 14852 Z= 0.304 Chirality : 0.038 0.113 1784 Planarity : 0.011 0.304 1872 Dihedral : 5.123 46.298 1536 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.23), residues: 1412 helix: -0.58 (0.19), residues: 716 sheet: -2.51 (0.68), residues: 48 loop : -1.62 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 252 TYR 0.038 0.002 TYR D 215 PHE 0.017 0.001 PHE D 115 TRP 0.020 0.001 TRP B 206 HIS 0.006 0.003 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10880) covalent geometry : angle 0.58042 / 0.30 (14852) hydrogen bonds : bond 0.02982 / 1.97 ( 480) hydrogen bonds : angle 5.21318 / 3.79 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.90 seconds wall clock time: 37 minutes 32.30 seconds (2252.30 seconds total)