Starting phenix.real_space_refine on Wed Mar 4 07:50:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s6v_10107/03_2026/6s6v_10107.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s6v_10107/03_2026/6s6v_10107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s6v_10107/03_2026/6s6v_10107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s6v_10107/03_2026/6s6v_10107.map" model { file = "/net/cci-nas-00/data/ceres_data/6s6v_10107/03_2026/6s6v_10107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s6v_10107/03_2026/6s6v_10107.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 7433 2.51 5 N 2079 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11820 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3047 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3041 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 7, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2828 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 7, 'TRANS': 355} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 62 residue: pdb=" N ASP A 119 " occ=0.83 ... (6 atoms not shown) pdb=" OD2 ASP A 119 " occ=0.65 residue: pdb=" N GLY A 120 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY A 120 " occ=0.94 residue: pdb=" N THR A 203 " occ=0.90 ... (5 atoms not shown) pdb=" CG2 THR A 203 " occ=0.90 residue: pdb=" N ASP A 247 " occ=0.73 ... (6 atoms not shown) pdb=" OD2 ASP A 247 " occ=0.58 residue: pdb=" N CYS A 249 " occ=0.67 ... (4 atoms not shown) pdb=" SG CYS A 249 " occ=0.79 residue: pdb=" N GLY A 250 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY A 250 " occ=0.88 residue: pdb=" N PRO A 278 " occ=0.97 ... (5 atoms not shown) pdb=" CD PRO A 278 " occ=0.97 residue: pdb=" N ALA A 280 " occ=0.84 ... (3 atoms not shown) pdb=" CB ALA A 280 " occ=0.84 residue: pdb=" N VAL A 281 " occ=0.91 ... (5 atoms not shown) pdb=" CG2 VAL A 281 " occ=0.91 residue: pdb=" N LEU A 282 " occ=0.60 ... (6 atoms not shown) pdb=" CD2 LEU A 282 " occ=0.60 residue: pdb=" N LYS A 283 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS A 283 " occ=0.50 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 ... (remaining 50 not shown) Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 11820 At special positions: 0 Unit cell: (104.94, 110.24, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 36 16.00 P 6 15.00 Mg 2 11.99 O 2260 8.00 N 2079 7.00 C 7433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 528.6 milliseconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 39.9% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.643A pdb=" N ARG A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 3.793A pdb=" N LEU A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 173 removed outlier: 3.734A pdb=" N GLY A 173 " --> pdb=" O CYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 295 through 298 removed outlier: 4.593A pdb=" N ASP A 298 " --> pdb=" O GLN A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 341 through 348 removed outlier: 3.685A pdb=" N ARG A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.596A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 4.491A pdb=" N GLN A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 56 through 71 removed outlier: 3.616A pdb=" N ARG B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.728A pdb=" N LEU B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 100 Processing helix chain 'B' and resid 149 through 173 removed outlier: 3.848A pdb=" N GLY B 173 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 314 through 318 removed outlier: 4.223A pdb=" N LEU B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS B 318 " --> pdb=" O GLU B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 318' Processing helix chain 'B' and resid 319 through 328 removed outlier: 3.549A pdb=" N LYS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 removed outlier: 4.196A pdb=" N ARG B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.963A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 393 removed outlier: 3.523A pdb=" N LEU B 383 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS B 392 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 removed outlier: 4.329A pdb=" N SER C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 removed outlier: 4.111A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.741A pdb=" N ALA C 160 " --> pdb=" O GLN C 157 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE C 161 " --> pdb=" O PHE C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'C' and resid 180 through 194 removed outlier: 3.676A pdb=" N SER C 186 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N PHE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 887 Processing helix chain 'C' and resid 893 through 919 removed outlier: 4.721A pdb=" N ARG C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 918 " --> pdb=" O GLN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 951 Processing helix chain 'C' and resid 952 through 970 Processing helix chain 'C' and resid 990 through 1000 Processing helix chain 'C' and resid 1001 through 1007 removed outlier: 3.782A pdb=" N LEU C1004 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C1006 " --> pdb=" O ALA C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 removed outlier: 3.541A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1046 removed outlier: 3.724A pdb=" N ALA C1046 " --> pdb=" O SER C1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.000A pdb=" N SER D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 3.953A pdb=" N LEU D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 140 Processing helix chain 'D' and resid 143 through 151 removed outlier: 4.290A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.707A pdb=" N ALA D 160 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 161' Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 180 through 193 removed outlier: 4.108A pdb=" N SER D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 887 Processing helix chain 'D' and resid 892 through 919 removed outlier: 3.536A pdb=" N ARG D 896 " --> pdb=" O GLY D 892 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 918 " --> pdb=" O GLN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 951 removed outlier: 3.780A pdb=" N THR D 950 " --> pdb=" O ASP D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 969 Processing helix chain 'D' and resid 990 through 1001 removed outlier: 4.581A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1005 removed outlier: 3.565A pdb=" N ASN D1005 " --> pdb=" O ASP D1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1002 through 1005' Processing helix chain 'D' and resid 1019 through 1024 removed outlier: 4.023A pdb=" N ARG D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 105 removed outlier: 4.184A pdb=" N ALA A 42 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 255 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 270 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 257 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 268 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 259 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.676A pdb=" N GLN A 113 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 124 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 179 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA A 219 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 181 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 218 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 282 removed outlier: 6.151A pdb=" N LEU A 282 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE A 309 " --> pdb=" O ARG A 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.799A pdb=" N ARG B 2 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE B 44 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 4 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL B 255 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 270 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU B 257 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 268 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B 259 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 113 through 116 removed outlier: 3.952A pdb=" N ALA B 124 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 182 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 179 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA B 219 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 181 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 236 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 279 through 282 removed outlier: 7.248A pdb=" N ALA B 280 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU B 310 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 282 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU B 307 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 337 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 21 removed outlier: 5.645A pdb=" N ILE C 3 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU C 86 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 5 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.587A pdb=" N LEU C 980 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE C1014 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 982 " --> pdb=" O ILE C1014 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE C 33 " --> pdb=" O VAL C1013 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 922 through 926 Processing sheet with id=AB1, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 21 removed outlier: 5.557A pdb=" N ILE D 3 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU D 86 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 5 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 115 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 116 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 980 through 981 removed outlier: 6.051A pdb=" N LEU D 980 " --> pdb=" O GLY D1012 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D1014 " --> pdb=" O LEU D 980 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 33 " --> pdb=" O VAL D1013 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 922 through 926 Processing sheet with id=AB5, first strand: chain 'D' and resid 1031 through 1032 440 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4068 1.36 - 1.51: 3810 1.51 - 1.65: 4098 1.65 - 1.80: 38 1.80 - 1.94: 16 Bond restraints: 12030 Sorted by residual: bond pdb=" CG LEU D1041 " pdb=" CD1 LEU D1041 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" N LYS D 890 " pdb=" CA LYS D 890 " ideal model delta sigma weight residual 1.468 1.444 0.024 1.24e-02 6.50e+03 3.65e+00 bond pdb=" CB VAL B 333 " pdb=" CG2 VAL B 333 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CB TRP A 9 " pdb=" CG TRP A 9 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 bond pdb=" CB GLU D 935 " pdb=" CG GLU D 935 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 ... (remaining 12025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 15607 1.97 - 3.93: 627 3.93 - 5.90: 58 5.90 - 7.87: 18 7.87 - 9.84: 11 Bond angle restraints: 16321 Sorted by residual: angle pdb=" CA THR D 975 " pdb=" CB THR D 975 " pdb=" CG2 THR D 975 " ideal model delta sigma weight residual 110.50 118.00 -7.50 1.70e+00 3.46e-01 1.95e+01 angle pdb=" N GLU C 25 " pdb=" CA GLU C 25 " pdb=" C GLU C 25 " ideal model delta sigma weight residual 109.81 118.67 -8.86 2.21e+00 2.05e-01 1.61e+01 angle pdb=" C ALA C 101 " pdb=" N ARG C 102 " pdb=" CA ARG C 102 " ideal model delta sigma weight residual 122.07 127.26 -5.19 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C LYS D 974 " pdb=" N THR D 975 " pdb=" CA THR D 975 " ideal model delta sigma weight residual 122.78 128.27 -5.49 1.52e+00 4.33e-01 1.31e+01 angle pdb=" CA GLU C 25 " pdb=" C GLU C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 118.44 124.12 -5.68 1.59e+00 3.96e-01 1.28e+01 ... (remaining 16316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.61: 6586 20.61 - 41.22: 582 41.22 - 61.82: 83 61.82 - 82.43: 15 82.43 - 103.04: 3 Dihedral angle restraints: 7269 sinusoidal: 2929 harmonic: 4340 Sorted by residual: dihedral pdb=" CA ALA C 942 " pdb=" C ALA C 942 " pdb=" N ASP C 943 " pdb=" CA ASP C 943 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA HIS B 392 " pdb=" C HIS B 392 " pdb=" N THR B 393 " pdb=" CA THR B 393 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG B 339 " pdb=" C ARG B 339 " pdb=" N ARG B 340 " pdb=" CA ARG B 340 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 7266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1419 0.061 - 0.121: 397 0.121 - 0.182: 58 0.182 - 0.242: 10 0.242 - 0.303: 2 Chirality restraints: 1886 Sorted by residual: chirality pdb=" CB VAL B 333 " pdb=" CA VAL B 333 " pdb=" CG1 VAL B 333 " pdb=" CG2 VAL B 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA THR D 975 " pdb=" N THR D 975 " pdb=" C THR D 975 " pdb=" CB THR D 975 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL D 114 " pdb=" CA VAL D 114 " pdb=" CG1 VAL D 114 " pdb=" CG2 VAL D 114 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1883 not shown) Planarity restraints: 2101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 111 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO D 112 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 133 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 134 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 58 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 59 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " 0.032 5.00e-02 4.00e+02 ... (remaining 2098 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 84 2.44 - 3.06: 7063 3.06 - 3.67: 17807 3.67 - 4.29: 25680 4.29 - 4.90: 43650 Nonbonded interactions: 94284 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.827 2.320 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 502 " model vdw 1.835 2.320 nonbonded pdb=" OD1 ASP A 8 " pdb="MN MN A 501 " model vdw 1.880 2.320 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 501 " model vdw 1.901 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.951 2.320 ... (remaining 94279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 139 or resid 149 through 502)) selection = (chain 'B' and (resid 1 through 139 or resid 149 through 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 194 or resid 880 through 1102)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.97 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: 0.010 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 0.072 12034 Z= 0.386 Angle : 0.907 9.837 16321 Z= 0.489 Chirality : 0.056 0.303 1886 Planarity : 0.007 0.071 2101 Dihedral : 15.548 103.038 4453 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.24 % Allowed : 12.64 % Favored : 87.13 % 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: -3.61 (0.19), residues: 1478 helix: -2.49 (0.16), residues: 495 sheet: -2.51 (0.27), residues: 298 loop : -2.12 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 946 TYR 0.017 0.002 TYR B 63 PHE 0.016 0.002 PHE D 33 TRP 0.008 0.002 TRP D 96 HIS 0.022 0.002 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00880 (12030) covalent geometry : angle 0.90706 (16321) hydrogen bonds : bond 0.18892 ( 440) hydrogen bonds : angle 7.85842 ( 1254) Misc. bond : bond 0.00294 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.7382 (ptp) cc_final: 0.6876 (ptp) REVERT: B 232 MET cc_start: 0.7217 (mtp) cc_final: 0.6986 (mtp) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.1738 time to fit residues: 20.5636 Evaluate side-chains 51 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 367 ASN B 25 GLN B 164 HIS B 227 GLN B 367 ASN B 384 GLN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.060507 restraints weight = 35610.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062447 restraints weight = 20551.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063742 restraints weight = 14601.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064517 restraints weight = 11755.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065103 restraints weight = 10276.763| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12034 Z= 0.133 Angle : 0.574 7.623 16321 Z= 0.300 Chirality : 0.042 0.146 1886 Planarity : 0.005 0.053 2101 Dihedral : 7.960 121.464 1654 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.41 % Allowed : 14.13 % Favored : 84.46 % 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: -2.25 (0.21), residues: 1478 helix: -0.65 (0.21), residues: 515 sheet: -2.26 (0.29), residues: 287 loop : -1.71 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 322 TYR 0.023 0.001 TYR C 55 PHE 0.007 0.001 PHE A 260 TRP 0.015 0.001 TRP C 880 HIS 0.004 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00281 (12030) covalent geometry : angle 0.57369 (16321) hydrogen bonds : bond 0.04201 ( 440) hydrogen bonds : angle 5.54063 ( 1254) Misc. bond : bond 0.00134 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7212 (ptpp) cc_final: 0.6977 (ptpt) REVERT: B 232 MET cc_start: 0.7297 (mtp) cc_final: 0.7076 (mtp) REVERT: C 182 TYR cc_start: 0.8542 (m-80) cc_final: 0.8198 (m-80) outliers start: 18 outliers final: 8 residues processed: 80 average time/residue: 0.1080 time to fit residues: 12.9794 Evaluate side-chains 62 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.0970 chunk 35 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 91 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.054092 restraints weight = 36756.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.055937 restraints weight = 20807.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.057168 restraints weight = 14667.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057748 restraints weight = 11782.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.058215 restraints weight = 10432.581| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12034 Z= 0.219 Angle : 0.597 9.658 16321 Z= 0.306 Chirality : 0.043 0.156 1886 Planarity : 0.004 0.046 2101 Dihedral : 7.673 133.867 1653 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.81 % Allowed : 14.68 % Favored : 83.52 % 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: -1.59 (0.22), residues: 1478 helix: 0.12 (0.22), residues: 522 sheet: -2.10 (0.29), residues: 291 loop : -1.42 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.021 0.002 TYR C 55 PHE 0.008 0.001 PHE C 95 TRP 0.008 0.001 TRP D 18 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00495 (12030) covalent geometry : angle 0.59704 (16321) hydrogen bonds : bond 0.04127 ( 440) hydrogen bonds : angle 5.15009 ( 1254) Misc. bond : bond 0.00165 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7590 (ptpp) cc_final: 0.7353 (ptpt) REVERT: B 192 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8360 (tmtt) REVERT: B 271 LEU cc_start: 0.8792 (pp) cc_final: 0.8522 (pp) REVERT: C 24 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7928 (tpp80) REVERT: D 1038 TYR cc_start: 0.8104 (m-10) cc_final: 0.7858 (m-10) outliers start: 23 outliers final: 16 residues processed: 78 average time/residue: 0.1096 time to fit residues: 12.7923 Evaluate side-chains 64 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055926 restraints weight = 36346.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057789 restraints weight = 20351.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.059099 restraints weight = 14293.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059795 restraints weight = 11356.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060263 restraints weight = 9902.220| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12034 Z= 0.111 Angle : 0.519 9.330 16321 Z= 0.266 Chirality : 0.041 0.151 1886 Planarity : 0.004 0.046 2101 Dihedral : 7.278 137.090 1652 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.96 % Allowed : 15.54 % Favored : 82.50 % 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: -1.09 (0.23), residues: 1478 helix: 0.67 (0.23), residues: 517 sheet: -1.75 (0.30), residues: 280 loop : -1.31 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 322 TYR 0.023 0.001 TYR C 55 PHE 0.009 0.001 PHE C 95 TRP 0.007 0.001 TRP D 18 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00241 (12030) covalent geometry : angle 0.51934 (16321) hydrogen bonds : bond 0.03446 ( 440) hydrogen bonds : angle 4.87282 ( 1254) Misc. bond : bond 0.00103 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7499 (pp) REVERT: B 149 LYS cc_start: 0.7543 (ptpp) cc_final: 0.7265 (ptpt) REVERT: B 192 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8273 (tmtt) REVERT: B 271 LEU cc_start: 0.8734 (pp) cc_final: 0.8508 (pp) REVERT: C 182 TYR cc_start: 0.8603 (m-80) cc_final: 0.8277 (m-80) REVERT: C 941 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7222 (mt0) outliers start: 25 outliers final: 14 residues processed: 79 average time/residue: 0.0985 time to fit residues: 11.9429 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 941 GLN Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056046 restraints weight = 36170.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.057938 restraints weight = 20247.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.059229 restraints weight = 14094.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059821 restraints weight = 11221.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.060337 restraints weight = 9879.503| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12034 Z= 0.119 Angle : 0.535 10.273 16321 Z= 0.268 Chirality : 0.042 0.271 1886 Planarity : 0.003 0.042 2101 Dihedral : 7.066 140.274 1652 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.04 % Allowed : 16.80 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1478 helix: 1.01 (0.23), residues: 512 sheet: -1.64 (0.30), residues: 282 loop : -1.18 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 322 TYR 0.022 0.001 TYR D 55 PHE 0.009 0.001 PHE C 95 TRP 0.007 0.001 TRP D 18 HIS 0.003 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00264 (12030) covalent geometry : angle 0.53528 (16321) hydrogen bonds : bond 0.03337 ( 440) hydrogen bonds : angle 4.74059 ( 1254) Misc. bond : bond 0.00108 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 126 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7551 (pp) REVERT: B 149 LYS cc_start: 0.7484 (ptpp) cc_final: 0.7191 (ptpt) REVERT: B 192 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8233 (tmtt) REVERT: B 271 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8518 (pp) REVERT: C 182 TYR cc_start: 0.8564 (m-80) cc_final: 0.8252 (m-80) outliers start: 26 outliers final: 21 residues processed: 79 average time/residue: 0.0939 time to fit residues: 11.5401 Evaluate side-chains 75 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053887 restraints weight = 36697.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.055675 restraints weight = 20680.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056907 restraints weight = 14556.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057518 restraints weight = 11657.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.058188 restraints weight = 10247.149| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12034 Z= 0.242 Angle : 0.612 9.205 16321 Z= 0.307 Chirality : 0.044 0.257 1886 Planarity : 0.004 0.043 2101 Dihedral : 7.255 149.475 1652 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.59 % Allowed : 17.27 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1478 helix: 1.01 (0.23), residues: 516 sheet: -1.80 (0.29), residues: 303 loop : -1.05 (0.26), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.024 0.002 TYR C 55 PHE 0.009 0.001 PHE C 95 TRP 0.007 0.001 TRP D 18 HIS 0.007 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00549 (12030) covalent geometry : angle 0.61168 (16321) hydrogen bonds : bond 0.03840 ( 440) hydrogen bonds : angle 4.84656 ( 1254) Misc. bond : bond 0.00173 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 126 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7619 (pp) REVERT: B 149 LYS cc_start: 0.7551 (ptpp) cc_final: 0.7288 (ptpt) REVERT: B 192 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8320 (tmtt) REVERT: C 190 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7377 (t80) REVERT: D 151 MET cc_start: 0.8618 (tpp) cc_final: 0.8164 (ttt) outliers start: 33 outliers final: 25 residues processed: 78 average time/residue: 0.0924 time to fit residues: 11.5192 Evaluate side-chains 76 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.055571 restraints weight = 36162.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.057439 restraints weight = 20306.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.058702 restraints weight = 14195.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.059376 restraints weight = 11351.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.059831 restraints weight = 9935.417| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12034 Z= 0.118 Angle : 0.529 8.108 16321 Z= 0.263 Chirality : 0.041 0.246 1886 Planarity : 0.004 0.046 2101 Dihedral : 7.041 146.263 1652 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.28 % Allowed : 17.90 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.23), residues: 1478 helix: 1.28 (0.23), residues: 513 sheet: -1.59 (0.30), residues: 285 loop : -1.06 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 340 TYR 0.024 0.001 TYR C 55 PHE 0.009 0.001 PHE C 95 TRP 0.008 0.001 TRP D 18 HIS 0.004 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00260 (12030) covalent geometry : angle 0.52927 (16321) hydrogen bonds : bond 0.03266 ( 440) hydrogen bonds : angle 4.65713 ( 1254) Misc. bond : bond 0.00117 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5888 (ptpp) REVERT: B 126 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7533 (pp) REVERT: B 149 LYS cc_start: 0.7473 (ptpp) cc_final: 0.7178 (ptpt) REVERT: B 192 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8221 (tmtt) REVERT: C 182 TYR cc_start: 0.8574 (m-80) cc_final: 0.8266 (m-80) REVERT: C 190 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7447 (t80) outliers start: 29 outliers final: 20 residues processed: 78 average time/residue: 0.0958 time to fit residues: 11.8428 Evaluate side-chains 75 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 973 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055812 restraints weight = 36261.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057685 restraints weight = 20251.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058944 restraints weight = 14061.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.059545 restraints weight = 11202.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.060087 restraints weight = 9828.318| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12034 Z= 0.125 Angle : 0.538 15.000 16321 Z= 0.265 Chirality : 0.041 0.146 1886 Planarity : 0.003 0.045 2101 Dihedral : 6.953 147.726 1652 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.20 % Allowed : 18.45 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1478 helix: 1.39 (0.23), residues: 515 sheet: -1.51 (0.31), residues: 285 loop : -1.01 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.025 0.001 TYR C 55 PHE 0.010 0.001 PHE D 95 TRP 0.009 0.001 TRP D 18 HIS 0.004 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00281 (12030) covalent geometry : angle 0.53831 (16321) hydrogen bonds : bond 0.03210 ( 440) hydrogen bonds : angle 4.55597 ( 1254) Misc. bond : bond 0.00105 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5960 (ptpp) REVERT: B 126 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7541 (pp) REVERT: B 149 LYS cc_start: 0.7419 (ptpp) cc_final: 0.7117 (ptpt) REVERT: B 170 LYS cc_start: 0.7817 (mmmt) cc_final: 0.7402 (mmtt) REVERT: B 192 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8189 (tmtt) REVERT: B 271 LEU cc_start: 0.8796 (pp) cc_final: 0.8579 (pp) REVERT: C 182 TYR cc_start: 0.8590 (m-80) cc_final: 0.8296 (m-80) REVERT: C 190 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7454 (t80) outliers start: 28 outliers final: 22 residues processed: 79 average time/residue: 0.0982 time to fit residues: 12.0585 Evaluate side-chains 80 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 117 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056092 restraints weight = 35955.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.057976 restraints weight = 20103.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059104 restraints weight = 14004.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059898 restraints weight = 11301.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.060530 restraints weight = 9788.941| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12034 Z= 0.120 Angle : 0.535 13.398 16321 Z= 0.265 Chirality : 0.041 0.146 1886 Planarity : 0.003 0.046 2101 Dihedral : 6.912 147.642 1652 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.35 % Allowed : 18.68 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1478 helix: 1.44 (0.23), residues: 515 sheet: -1.47 (0.31), residues: 289 loop : -0.93 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 74 TYR 0.025 0.001 TYR D 55 PHE 0.009 0.001 PHE D 95 TRP 0.008 0.001 TRP C 880 HIS 0.005 0.001 HIS D 973 Details of bonding type rmsd covalent geometry : bond 0.00268 (12030) covalent geometry : angle 0.53469 (16321) hydrogen bonds : bond 0.03167 ( 440) hydrogen bonds : angle 4.50041 ( 1254) Misc. bond : bond 0.00114 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5929 (ptpp) REVERT: B 126 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7522 (pp) REVERT: B 149 LYS cc_start: 0.7352 (ptpp) cc_final: 0.7049 (ptpt) REVERT: B 170 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7390 (mmtt) REVERT: B 271 LEU cc_start: 0.8749 (pp) cc_final: 0.8526 (pp) REVERT: C 182 TYR cc_start: 0.8572 (m-80) cc_final: 0.8285 (m-80) REVERT: C 190 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7463 (t80) REVERT: C 935 GLU cc_start: 0.7891 (pm20) cc_final: 0.7612 (pm20) outliers start: 30 outliers final: 24 residues processed: 83 average time/residue: 0.0948 time to fit residues: 12.1817 Evaluate side-chains 79 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 138 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 0.0050 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.057325 restraints weight = 36116.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.059208 restraints weight = 20400.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060478 restraints weight = 14313.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061080 restraints weight = 11456.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061494 restraints weight = 10120.634| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12034 Z= 0.093 Angle : 0.539 13.963 16321 Z= 0.264 Chirality : 0.041 0.147 1886 Planarity : 0.003 0.047 2101 Dihedral : 6.775 144.993 1652 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.88 % Allowed : 19.23 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.23), residues: 1478 helix: 1.59 (0.24), residues: 511 sheet: -1.40 (0.31), residues: 278 loop : -0.86 (0.26), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.023 0.001 TYR D 55 PHE 0.010 0.001 PHE C 95 TRP 0.011 0.001 TRP C 880 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00203 (12030) covalent geometry : angle 0.53857 (16321) hydrogen bonds : bond 0.02939 ( 440) hydrogen bonds : angle 4.40336 ( 1254) Misc. bond : bond 0.00088 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.6174 (OUTLIER) cc_final: 0.5785 (ptpt) REVERT: B 170 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7401 (mmtt) REVERT: B 271 LEU cc_start: 0.8755 (pp) cc_final: 0.8551 (pp) REVERT: C 182 TYR cc_start: 0.8576 (m-80) cc_final: 0.8310 (m-80) REVERT: C 190 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 935 GLU cc_start: 0.7794 (pm20) cc_final: 0.7470 (pm20) outliers start: 24 outliers final: 18 residues processed: 81 average time/residue: 0.0892 time to fit residues: 11.2596 Evaluate side-chains 76 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 72 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.057587 restraints weight = 35730.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059513 restraints weight = 19918.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060802 restraints weight = 13852.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061615 restraints weight = 10981.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062042 restraints weight = 9481.405| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12034 Z= 0.092 Angle : 0.531 14.107 16321 Z= 0.259 Chirality : 0.041 0.145 1886 Planarity : 0.003 0.040 2101 Dihedral : 6.696 144.639 1652 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.73 % Allowed : 19.47 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1478 helix: 1.61 (0.23), residues: 518 sheet: -1.21 (0.31), residues: 286 loop : -0.81 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 74 TYR 0.024 0.001 TYR D 55 PHE 0.009 0.001 PHE D 95 TRP 0.009 0.001 TRP C 880 HIS 0.004 0.001 HIS D 973 Details of bonding type rmsd covalent geometry : bond 0.00202 (12030) covalent geometry : angle 0.53114 (16321) hydrogen bonds : bond 0.02919 ( 440) hydrogen bonds : angle 4.35244 ( 1254) Misc. bond : bond 0.00081 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.61 seconds wall clock time: 32 minutes 23.26 seconds (1943.26 seconds total)