Starting phenix.real_space_refine on Fri Sep 11 22:19:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s6v_10107/09_2026/6s6v_10107.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s6v_10107/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6s6v_10107/09_2026/6s6v_10107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s6v_10107/09_2026/6s6v_10107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s6v_10107/09_2026/6s6v_10107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s6v_10107/09_2026/6s6v_10107.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6s6v_10107/09_2026/6s6v_10107.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s6v_10107/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.60, per 1000 atoms: 0.22 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: 1.07 Conformation dependent library (CDL) restraints added in 653.6 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: 0.23 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: 1.78 Time building geometry restraints manager: 1.41 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: 6576 20.61 - 41.22: 579 41.22 - 61.82: 74 61.82 - 82.43: 15 82.43 - 103.04: 3 Dihedral angle restraints: 7247 sinusoidal: 2907 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 7244 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: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 : 15.368 103.038 4431 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/Z covalent geometry : bond 0.00880 / 0.39 (12030) covalent geometry : angle 0.90706 / 0.49 (16321) hydrogen bonds : bond 0.18892 / 12.98 ( 440) hydrogen bonds : angle 7.85842 / 5.51 ( 1254) Misc. bond : bond 0.00294 / 0.15 ( 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 : 0.333 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: 0.1499 time to fit residues: 17.8349 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 : 0.463 ------------------------------------------------------------------------------- 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... 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 = 0.3337 r_free = 0.3337 target = 0.078486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.060650 restraints weight = 35613.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062573 restraints weight = 20797.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063901 restraints weight = 14751.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064737 restraints weight = 11874.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065178 restraints weight = 10296.476| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 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 = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 12 (16 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1351 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= 0.132 Angle : 0.567 8.201 16321 Z= 0.296 Chirality : 0.042 0.146 1886 Planarity : 0.005 0.052 2101 Dihedral : 7.233 118.699 1632 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.49 % Allowed : 13.97 % Favored : 84.54 % 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: -2.24 (0.21), residues: 1478 helix: -0.61 (0.21), residues: 515 sheet: -2.29 (0.28), residues: 289 loop : -1.70 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 322 TYR 0.025 0.001 TYR C 55 PHE 0.008 0.001 PHE A 260 TRP 0.017 0.001 TRP C 880 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12030) covalent geometry : angle 0.56713 / 0.30 (16321) hydrogen bonds : bond 0.04065 / 2.76 ( 440) hydrogen bonds : angle 5.46876 / 3.84 ( 1254) Misc. bond : bond 0.00151 / 0.08 ( 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 88 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7277 (ptpp) cc_final: 0.7035 (ptpt) REVERT: B 232 MET cc_start: 0.7318 (mtp) cc_final: 0.7102 (mtp) REVERT: C 182 TYR cc_start: 0.8540 (m-80) cc_final: 0.8208 (m-80) outliers start: 19 outliers final: 6 residues processed: 83 average time/residue: 0.1029 time to fit residues: 13.0372 Evaluate side-chains 62 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 134 GLU 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: 1.9990 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.073399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.056385 restraints weight = 36107.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058275 restraints weight = 20128.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.059552 restraints weight = 14031.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.060107 restraints weight = 11160.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060810 restraints weight = 9872.695| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12034 Z= 0.119 Angle : 0.532 9.947 16321 Z= 0.272 Chirality : 0.041 0.153 1886 Planarity : 0.004 0.067 2101 Dihedral : 6.929 126.151 1631 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.49 % Allowed : 14.76 % Favored : 83.75 % 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: -1.43 (0.22), residues: 1478 helix: 0.35 (0.23), residues: 509 sheet: -1.88 (0.30), residues: 272 loop : -1.48 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 322 TYR 0.021 0.001 TYR C 55 PHE 0.009 0.001 PHE C 95 TRP 0.008 0.001 TRP A 306 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12030) covalent geometry : angle 0.53171 / 0.27 (16321) hydrogen bonds : bond 0.03610 / 2.47 ( 440) hydrogen bonds : angle 4.98655 / 3.48 ( 1254) Misc. bond : bond 0.00107 / 0.05 ( 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 84 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7332 (ptpp) cc_final: 0.7071 (ptpt) REVERT: B 192 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8208 (tmtt) REVERT: B 232 MET cc_start: 0.7279 (mtp) cc_final: 0.7061 (mtp) REVERT: C 182 TYR cc_start: 0.8581 (m-80) cc_final: 0.8274 (m-80) REVERT: D 72 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8142 (ttp) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.0988 time to fit residues: 12.0442 Evaluate side-chains 71 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 D residue 72 MET Chi-restraints excluded: chain D residue 87 VAL 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: 0.0370 chunk 128 optimal weight: 0.7980 chunk 66 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 86 optimal weight: 0.0570 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3300 r_free = 0.3300 target = 0.074499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056903 restraints weight = 35987.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059004 restraints weight = 19374.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060401 restraints weight = 13084.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.061187 restraints weight = 10226.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061826 restraints weight = 8832.911| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- 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: 53 | |-----------------------------------------------------------------------------| |-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: 54 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12034 Z= 0.091 Angle : 0.498 9.279 16321 Z= 0.254 Chirality : 0.040 0.200 1886 Planarity : 0.003 0.043 2101 Dihedral : 6.732 129.929 1630 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.57 % Allowed : 16.01 % Favored : 82.42 % 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: -0.98 (0.22), residues: 1478 helix: 0.81 (0.23), residues: 512 sheet: -1.60 (0.31), residues: 264 loop : -1.33 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.023 0.001 TYR C 55 PHE 0.008 0.001 PHE C 95 TRP 0.008 0.001 TRP C 880 HIS 0.004 0.001 HIS D 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (12030) covalent geometry : angle 0.49778 / 0.25 (16321) hydrogen bonds : bond 0.03118 / 2.10 ( 440) hydrogen bonds : angle 4.72196 / 3.28 ( 1254) Misc. bond : bond 0.00085 / 0.04 ( 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 85 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7394 (pp) REVERT: B 149 LYS cc_start: 0.7538 (ptpp) cc_final: 0.7262 (ptpt) REVERT: B 192 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8260 (tmtt) REVERT: B 232 MET cc_start: 0.7234 (mtp) cc_final: 0.7006 (mtp) REVERT: B 271 LEU cc_start: 0.8698 (pp) cc_final: 0.8448 (pp) REVERT: C 182 TYR cc_start: 0.8695 (m-80) cc_final: 0.8425 (m-80) outliers start: 20 outliers final: 12 residues processed: 82 average time/residue: 0.0869 time to fit residues: 11.4892 Evaluate side-chains 69 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 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 988 THR 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: 7.9990 chunk 24 optimal weight: 0.3980 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 941 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056976 restraints weight = 36150.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058843 restraints weight = 20078.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.060123 restraints weight = 13954.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060755 restraints weight = 11085.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061456 restraints weight = 9688.832| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-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: 53 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12034 Z= 0.119 Angle : 0.530 13.096 16321 Z= 0.261 Chirality : 0.041 0.232 1886 Planarity : 0.003 0.041 2101 Dihedral : 6.711 133.307 1630 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.57 % Allowed : 16.72 % Favored : 81.71 % 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: -0.71 (0.23), residues: 1478 helix: 1.12 (0.23), residues: 512 sheet: -1.52 (0.30), residues: 276 loop : -1.20 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.020 0.001 TYR D 55 PHE 0.009 0.001 PHE C 95 TRP 0.007 0.001 TRP C 880 HIS 0.004 0.001 HIS D 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12030) covalent geometry : angle 0.52981 / 0.26 (16321) hydrogen bonds : bond 0.03154 / 2.12 ( 440) hydrogen bonds : angle 4.62886 / 3.21 ( 1254) Misc. bond : bond 0.00113 / 0.06 ( 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 79 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7427 (pp) REVERT: B 149 LYS cc_start: 0.7268 (ptpp) cc_final: 0.6992 (ptpt) REVERT: B 192 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8239 (tmtt) REVERT: B 232 MET cc_start: 0.7228 (mtp) cc_final: 0.7014 (mtp) REVERT: B 271 LEU cc_start: 0.8678 (pp) cc_final: 0.8440 (pp) REVERT: C 182 TYR cc_start: 0.8549 (m-80) cc_final: 0.8278 (m-80) REVERT: D 125 LEU cc_start: 0.8976 (mm) cc_final: 0.8768 (mp) outliers start: 20 outliers final: 18 residues processed: 74 average time/residue: 0.1011 time to fit residues: 11.4732 Evaluate side-chains 76 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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 988 THR Chi-restraints excluded: chain D residue 87 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 145 optimal weight: 0.0000 chunk 54 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 2.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054581 restraints weight = 36627.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.056397 restraints weight = 20729.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057647 restraints weight = 14574.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058402 restraints weight = 11618.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059024 restraints weight = 10136.854| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12034 Z= 0.220 Angle : 0.590 11.369 16321 Z= 0.295 Chirality : 0.043 0.256 1886 Planarity : 0.004 0.042 2101 Dihedral : 6.885 138.945 1630 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.88 % Allowed : 17.19 % Favored : 80.93 % 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: -0.64 (0.23), residues: 1478 helix: 1.20 (0.23), residues: 511 sheet: -1.72 (0.29), residues: 298 loop : -1.01 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.025 0.002 TYR C 55 PHE 0.008 0.001 PHE D 95 TRP 0.006 0.001 TRP D 18 HIS 0.006 0.001 HIS D1016 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (12030) covalent geometry : angle 0.59043 / 0.29 (16321) hydrogen bonds : bond 0.03573 / 2.38 ( 440) hydrogen bonds : angle 4.71419 / 3.27 ( 1254) Misc. bond : bond 0.00181 / 0.09 ( 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 78 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7533 (pp) REVERT: B 149 LYS cc_start: 0.7423 (ptpp) cc_final: 0.7172 (ptpt) REVERT: B 192 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8342 (tmtt) REVERT: C 182 TYR cc_start: 0.8609 (m-80) cc_final: 0.8299 (m-80) outliers start: 24 outliers final: 21 residues processed: 74 average time/residue: 0.0934 time to fit residues: 10.6792 Evaluate side-chains 71 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 3 ILE 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 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 87 VAL 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: 7.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.072694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055599 restraints weight = 36326.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.057465 restraints weight = 20417.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058734 restraints weight = 14250.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.059321 restraints weight = 11362.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059816 restraints weight = 10037.823| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2127 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= 0.141 Angle : 0.536 10.901 16321 Z= 0.267 Chirality : 0.042 0.246 1886 Planarity : 0.004 0.044 2101 Dihedral : 6.773 137.533 1630 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.12 % Allowed : 17.27 % Favored : 80.61 % 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: -0.51 (0.23), residues: 1478 helix: 1.30 (0.23), residues: 515 sheet: -1.52 (0.30), residues: 288 loop : -1.04 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 60 TYR 0.024 0.001 TYR C 55 PHE 0.008 0.001 PHE C 95 TRP 0.007 0.001 TRP D 18 HIS 0.004 0.001 HIS D1016 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (12030) covalent geometry : angle 0.53633 / 0.27 (16321) hydrogen bonds : bond 0.03247 / 2.16 ( 440) hydrogen bonds : angle 4.60876 / 3.19 ( 1254) Misc. bond : bond 0.00129 / 0.07 ( 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: 27 poor density : 57 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7520 (pp) REVERT: B 149 LYS cc_start: 0.7425 (ptpp) cc_final: 0.7144 (ptpt) REVERT: C 182 TYR cc_start: 0.8568 (m-80) cc_final: 0.8273 (m-80) REVERT: C 190 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7406 (t80) outliers start: 27 outliers final: 20 residues processed: 78 average time/residue: 0.0847 time to fit residues: 10.5186 Evaluate side-chains 75 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 3 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3261 r_free = 0.3261 target = 0.072749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055604 restraints weight = 36411.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057475 restraints weight = 20440.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058738 restraints weight = 14307.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.059425 restraints weight = 11398.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.060089 restraints weight = 9961.293| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2192 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= 0.138 Angle : 0.556 15.479 16321 Z= 0.271 Chirality : 0.041 0.146 1886 Planarity : 0.004 0.045 2101 Dihedral : 6.721 138.573 1630 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.12 % Allowed : 17.66 % Favored : 80.22 % 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: -0.40 (0.23), residues: 1478 helix: 1.41 (0.24), residues: 514 sheet: -1.45 (0.31), residues: 284 loop : -1.01 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 60 TYR 0.025 0.001 TYR C 55 PHE 0.009 0.001 PHE C 95 TRP 0.009 0.001 TRP D 18 HIS 0.004 0.001 HIS D1016 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12030) covalent geometry : angle 0.55552 / 0.27 (16321) hydrogen bonds : bond 0.03201 / 2.12 ( 440) hydrogen bonds : angle 4.56191 / 3.14 ( 1254) Misc. bond : bond 0.00127 / 0.06 ( 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: 27 poor density : 56 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7510 (pp) REVERT: B 149 LYS cc_start: 0.7327 (ptpp) cc_final: 0.7051 (ptpt) REVERT: B 271 LEU cc_start: 0.8705 (pp) cc_final: 0.8470 (pp) REVERT: C 151 MET cc_start: 0.8667 (tpp) cc_final: 0.8209 (ttt) REVERT: C 182 TYR cc_start: 0.8579 (m-80) cc_final: 0.8290 (m-80) REVERT: C 190 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7484 (t80) outliers start: 27 outliers final: 21 residues processed: 78 average time/residue: 0.0770 time to fit residues: 9.6663 Evaluate side-chains 76 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.056518 restraints weight = 35896.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058423 restraints weight = 20132.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.059702 restraints weight = 14028.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060309 restraints weight = 11205.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060684 restraints weight = 9851.877| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12034 Z= 0.106 Angle : 0.543 13.965 16321 Z= 0.263 Chirality : 0.041 0.147 1886 Planarity : 0.003 0.046 2101 Dihedral : 6.614 138.473 1630 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.73 % Allowed : 18.13 % 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: -0.30 (0.23), residues: 1478 helix: 1.51 (0.24), residues: 515 sheet: -1.44 (0.31), residues: 284 loop : -0.93 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.026 0.001 TYR D 55 PHE 0.009 0.001 PHE C 95 TRP 0.011 0.001 TRP C 880 HIS 0.003 0.001 HIS B 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (12030) covalent geometry : angle 0.54262 / 0.26 (16321) hydrogen bonds : bond 0.03013 / 2.01 ( 440) hydrogen bonds : angle 4.45057 / 3.05 ( 1254) Misc. bond : bond 0.00093 / 0.05 ( 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 81 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7354 (ptpp) cc_final: 0.7064 (ptpt) REVERT: B 271 LEU cc_start: 0.8671 (pp) cc_final: 0.8463 (pp) REVERT: C 182 TYR cc_start: 0.8581 (m-80) cc_final: 0.8312 (m-80) outliers start: 22 outliers final: 20 residues processed: 76 average time/residue: 0.0819 time to fit residues: 10.0465 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS 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 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 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 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: 0.9980 chunk 10 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3288 r_free = 0.3288 target = 0.074109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.056823 restraints weight = 36237.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058712 restraints weight = 20361.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.060011 restraints weight = 14277.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060745 restraints weight = 11410.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061062 restraints weight = 9931.677| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12034 Z= 0.101 Angle : 0.543 14.799 16321 Z= 0.262 Chirality : 0.041 0.146 1886 Planarity : 0.003 0.039 2101 Dihedral : 6.574 139.386 1630 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.88 % Allowed : 18.45 % Favored : 79.67 % 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: -0.15 (0.23), residues: 1478 helix: 1.63 (0.24), residues: 514 sheet: -1.29 (0.31), residues: 289 loop : -0.86 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.025 0.001 TYR D 55 PHE 0.009 0.001 PHE C 95 TRP 0.011 0.001 TRP C 880 HIS 0.006 0.001 HIS D 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (12030) covalent geometry : angle 0.54254 / 0.26 (16321) hydrogen bonds : bond 0.02979 / 1.98 ( 440) hydrogen bonds : angle 4.41223 / 3.02 ( 1254) Misc. bond : bond 0.00097 / 0.05 ( 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 79 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 LEU cc_start: 0.8686 (pp) cc_final: 0.8484 (pp) REVERT: C 182 TYR cc_start: 0.8592 (m-80) cc_final: 0.8321 (m-80) outliers start: 24 outliers final: 19 residues processed: 74 average time/residue: 0.0923 time to fit residues: 10.7845 Evaluate side-chains 71 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS 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 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 1004 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.057033 restraints weight = 36335.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058931 restraints weight = 20221.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.060232 restraints weight = 14137.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060928 restraints weight = 11236.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061437 restraints weight = 9819.059| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12034 Z= 0.106 Angle : 0.543 14.556 16321 Z= 0.262 Chirality : 0.041 0.145 1886 Planarity : 0.003 0.039 2101 Dihedral : 6.550 140.618 1630 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.73 % Allowed : 18.60 % Favored : 79.67 % 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: -0.07 (0.23), residues: 1478 helix: 1.71 (0.24), residues: 511 sheet: -1.30 (0.31), residues: 295 loop : -0.78 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 60 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 0.003 0.001 HIS D1016 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12030) covalent geometry : angle 0.54274 / 0.26 (16321) hydrogen bonds : bond 0.02955 / 1.96 ( 440) hydrogen bonds : angle 4.37614 / 2.99 ( 1254) Misc. bond : bond 0.00120 / 0.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.09 seconds wall clock time: 30 minutes 11.09 seconds (1811.09 seconds total)