Starting phenix.real_space_refine on Wed Jul 30 04:12:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s6v_10107/07_2025/6s6v_10107.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s6v_10107/07_2025/6s6v_10107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s6v_10107/07_2025/6s6v_10107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s6v_10107/07_2025/6s6v_10107.map" model { file = "/net/cci-nas-00/data/ceres_data/6s6v_10107/07_2025/6s6v_10107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s6v_10107/07_2025/6s6v_10107.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.73, per 1000 atoms: 0.65 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: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.48 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: 3.40 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4068 1.36 - 1.51: 3810 1.51 - 1.65: 4098 1.65 - 1.80: 38 1.80 - 1.94: 16 Bond restraints: 12030 Sorted by residual: bond pdb=" CG LEU D1041 " pdb=" CD1 LEU D1041 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" N LYS D 890 " pdb=" CA LYS D 890 " ideal model delta sigma weight residual 1.468 1.444 0.024 1.24e-02 6.50e+03 3.65e+00 bond pdb=" CB VAL B 333 " pdb=" CG2 VAL B 333 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CB TRP A 9 " pdb=" CG TRP A 9 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 bond pdb=" CB GLU D 935 " pdb=" CG GLU D 935 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 ... (remaining 12025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 15607 1.97 - 3.93: 627 3.93 - 5.90: 58 5.90 - 7.87: 18 7.87 - 9.84: 11 Bond angle restraints: 16321 Sorted by residual: angle pdb=" CA THR D 975 " pdb=" CB THR D 975 " pdb=" CG2 THR D 975 " ideal model delta sigma weight residual 110.50 118.00 -7.50 1.70e+00 3.46e-01 1.95e+01 angle pdb=" N GLU C 25 " pdb=" CA GLU C 25 " pdb=" C GLU C 25 " ideal model delta sigma weight residual 109.81 118.67 -8.86 2.21e+00 2.05e-01 1.61e+01 angle pdb=" C ALA C 101 " pdb=" N ARG C 102 " pdb=" CA ARG C 102 " ideal model delta sigma weight residual 122.07 127.26 -5.19 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C LYS D 974 " pdb=" N THR D 975 " pdb=" CA THR D 975 " ideal model delta sigma weight residual 122.78 128.27 -5.49 1.52e+00 4.33e-01 1.31e+01 angle pdb=" CA GLU C 25 " pdb=" C GLU C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 118.44 124.12 -5.68 1.59e+00 3.96e-01 1.28e+01 ... (remaining 16316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.61: 6586 20.61 - 41.22: 582 41.22 - 61.82: 83 61.82 - 82.43: 15 82.43 - 103.04: 3 Dihedral angle restraints: 7269 sinusoidal: 2929 harmonic: 4340 Sorted by residual: dihedral pdb=" CA ALA C 942 " pdb=" C ALA C 942 " pdb=" N ASP C 943 " pdb=" CA ASP C 943 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA HIS B 392 " pdb=" C HIS B 392 " pdb=" N THR B 393 " pdb=" CA THR B 393 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG B 339 " pdb=" C ARG B 339 " pdb=" N ARG B 340 " pdb=" CA ARG B 340 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 7266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1419 0.061 - 0.121: 397 0.121 - 0.182: 58 0.182 - 0.242: 10 0.242 - 0.303: 2 Chirality restraints: 1886 Sorted by residual: chirality pdb=" CB VAL B 333 " pdb=" CA VAL B 333 " pdb=" CG1 VAL B 333 " pdb=" CG2 VAL B 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA THR D 975 " pdb=" N THR D 975 " pdb=" C THR D 975 " pdb=" CB THR D 975 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL D 114 " pdb=" CA VAL D 114 " pdb=" CG1 VAL D 114 " pdb=" CG2 VAL D 114 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1883 not shown) Planarity restraints: 2101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 111 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO D 112 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 133 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 134 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 58 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 59 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " 0.032 5.00e-02 4.00e+02 ... (remaining 2098 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 84 2.44 - 3.06: 7063 3.06 - 3.67: 17807 3.67 - 4.29: 25680 4.29 - 4.90: 43650 Nonbonded interactions: 94284 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.827 2.320 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 502 " model vdw 1.835 2.320 nonbonded pdb=" OD1 ASP A 8 " pdb="MN MN A 501 " model vdw 1.880 2.320 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 501 " model vdw 1.901 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.951 2.320 ... (remaining 94279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 139 or resid 149 through 395 or resid 501 throug \ h 502)) selection = (chain 'B' and (resid 1 through 139 or resid 149 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 194 or resid 880 through 1048 or resid 1101 thro \ ugh 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.570 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 12034 Z= 0.386 Angle : 0.907 9.837 16321 Z= 0.489 Chirality : 0.056 0.303 1886 Planarity : 0.007 0.071 2101 Dihedral : 15.548 103.038 4453 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP D 96 HIS 0.022 0.002 HIS B 5 PHE 0.016 0.002 PHE D 33 TYR 0.017 0.002 TYR B 63 ARG 0.006 0.001 ARG D 946 Details of bonding type rmsd hydrogen bonds : bond 0.18892 ( 440) hydrogen bonds : angle 7.85842 ( 1254) covalent geometry : bond 0.00880 (12030) covalent geometry : angle 0.90706 (16321) Misc. bond : bond 0.00294 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.382 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: 0.3590 time to fit residues: 42.7330 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 : 1.276 ------------------------------------------------------------------------------- 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 124 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 367 ASN B 25 GLN B 164 HIS B 227 GLN B 367 ASN B 384 GLN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060460 restraints weight = 35326.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062386 restraints weight = 20526.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.063663 restraints weight = 14632.114| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12034 Z= 0.133 Angle : 0.573 7.944 16321 Z= 0.298 Chirality : 0.042 0.147 1886 Planarity : 0.005 0.053 2101 Dihedral : 7.973 120.784 1654 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.33 % Allowed : 13.89 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1478 helix: -0.62 (0.21), residues: 515 sheet: -2.26 (0.29), residues: 287 loop : -1.71 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 880 HIS 0.004 0.001 HIS D1016 PHE 0.007 0.001 PHE A 260 TYR 0.023 0.001 TYR C 55 ARG 0.008 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 440) hydrogen bonds : angle 5.54814 ( 1254) covalent geometry : bond 0.00284 (12030) covalent geometry : angle 0.57291 (16321) Misc. bond : bond 0.00104 ( 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 84 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7351 (ptpp) cc_final: 0.7123 (ptpt) REVERT: B 232 MET cc_start: 0.7336 (mtp) cc_final: 0.7117 (mtp) outliers start: 17 outliers final: 6 residues processed: 80 average time/residue: 0.2427 time to fit residues: 29.1621 Evaluate side-chains 61 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 124 optimal weight: 8.9990 chunk 110 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 91 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.054299 restraints weight = 36562.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.056174 restraints weight = 20456.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057367 restraints weight = 14249.636| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12034 Z= 0.213 Angle : 0.594 9.234 16321 Z= 0.304 Chirality : 0.043 0.152 1886 Planarity : 0.004 0.046 2101 Dihedral : 7.664 133.437 1653 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.73 % Allowed : 14.84 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1478 helix: 0.13 (0.22), residues: 524 sheet: -2.12 (0.29), residues: 291 loop : -1.42 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 18 HIS 0.006 0.001 HIS D1016 PHE 0.008 0.001 PHE C 95 TYR 0.020 0.002 TYR C 55 ARG 0.002 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 440) hydrogen bonds : angle 5.14406 ( 1254) covalent geometry : bond 0.00482 (12030) covalent geometry : angle 0.59393 (16321) Misc. bond : bond 0.00156 ( 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 80 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7584 (ptpp) cc_final: 0.7348 (ptpt) REVERT: B 192 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8357 (tmtt) REVERT: B 271 LEU cc_start: 0.8793 (pp) cc_final: 0.8524 (pp) REVERT: C 24 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7878 (tpp80) outliers start: 22 outliers final: 15 residues processed: 77 average time/residue: 0.2233 time to fit residues: 26.4679 Evaluate side-chains 66 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 147 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 0.0040 chunk 129 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 941 GLN ** 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 = 0.3283 r_free = 0.3283 target = 0.073833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056835 restraints weight = 35847.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058700 restraints weight = 20035.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.060016 restraints weight = 14041.458| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- 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: 49 | |-----------------------------------------------------------------------------| |-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: 49 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12034 Z= 0.095 Angle : 0.508 8.768 16321 Z= 0.259 Chirality : 0.041 0.151 1886 Planarity : 0.004 0.045 2101 Dihedral : 7.162 137.353 1652 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.49 % Allowed : 16.33 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1478 helix: 0.88 (0.23), residues: 509 sheet: -1.65 (0.31), residues: 261 loop : -1.31 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 880 HIS 0.003 0.001 HIS B 5 PHE 0.009 0.001 PHE C 95 TYR 0.027 0.001 TYR C 55 ARG 0.002 0.000 ARG D 946 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 440) hydrogen bonds : angle 4.78059 ( 1254) covalent geometry : bond 0.00203 (12030) covalent geometry : angle 0.50812 (16321) Misc. bond : bond 0.00086 ( 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 87 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7463 (pp) REVERT: B 149 LYS cc_start: 0.7518 (ptpp) cc_final: 0.7224 (ptpt) REVERT: B 192 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8325 (tmtt) REVERT: B 271 LEU cc_start: 0.8734 (pp) cc_final: 0.8494 (pp) REVERT: C 24 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7972 (tpp80) REVERT: C 151 MET cc_start: 0.8523 (tpp) cc_final: 0.8287 (ttt) REVERT: C 182 TYR cc_start: 0.8595 (m-80) cc_final: 0.8297 (m-80) outliers start: 19 outliers final: 10 residues processed: 85 average time/residue: 0.2296 time to fit residues: 29.7223 Evaluate side-chains 70 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ILE 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 1011 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** 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 = 0.3272 r_free = 0.3272 target = 0.073283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.056174 restraints weight = 36140.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058040 restraints weight = 20379.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059360 restraints weight = 14217.335| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12034 Z= 0.119 Angle : 0.521 10.211 16321 Z= 0.261 Chirality : 0.042 0.241 1886 Planarity : 0.003 0.041 2101 Dihedral : 6.967 141.529 1652 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.88 % Allowed : 17.27 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1478 helix: 1.15 (0.23), residues: 509 sheet: -1.68 (0.30), residues: 277 loop : -1.14 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 880 HIS 0.005 0.001 HIS D 973 PHE 0.009 0.001 PHE C 95 TYR 0.020 0.001 TYR D 55 ARG 0.005 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 440) hydrogen bonds : angle 4.65559 ( 1254) covalent geometry : bond 0.00264 (12030) covalent geometry : angle 0.52093 (16321) Misc. bond : bond 0.00108 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7540 (pp) REVERT: B 149 LYS cc_start: 0.7510 (ptpp) cc_final: 0.7225 (ptpt) REVERT: B 192 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8228 (tmtt) REVERT: B 271 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8528 (pp) REVERT: C 151 MET cc_start: 0.8484 (tpp) cc_final: 0.8272 (ttt) REVERT: C 182 TYR cc_start: 0.8595 (m-80) cc_final: 0.8300 (m-80) outliers start: 24 outliers final: 20 residues processed: 74 average time/residue: 0.2485 time to fit residues: 27.4225 Evaluate side-chains 76 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain 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 271 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** 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 = 0.3257 r_free = 0.3257 target = 0.072483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055359 restraints weight = 36265.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057196 restraints weight = 20360.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058434 restraints weight = 14292.219| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12034 Z= 0.151 Angle : 0.532 9.875 16321 Z= 0.267 Chirality : 0.042 0.258 1886 Planarity : 0.004 0.046 2101 Dihedral : 6.976 145.498 1652 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.43 % Allowed : 16.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1478 helix: 1.28 (0.23), residues: 510 sheet: -1.63 (0.30), residues: 287 loop : -1.03 (0.26), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 18 HIS 0.004 0.001 HIS D1016 PHE 0.009 0.001 PHE C 95 TYR 0.023 0.001 TYR C 55 ARG 0.008 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 440) hydrogen bonds : angle 4.61453 ( 1254) covalent geometry : bond 0.00339 (12030) covalent geometry : angle 0.53176 (16321) Misc. bond : bond 0.00135 ( 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 85 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7516 (pp) REVERT: B 149 LYS cc_start: 0.7507 (ptpp) cc_final: 0.7222 (ptpt) REVERT: B 192 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8244 (tmtt) REVERT: C 182 TYR cc_start: 0.8625 (m-80) cc_final: 0.8322 (m-80) REVERT: C 190 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7477 (t80) outliers start: 31 outliers final: 24 residues processed: 79 average time/residue: 0.2098 time to fit residues: 26.4743 Evaluate side-chains 77 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 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 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** 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 = 0.3273 r_free = 0.3273 target = 0.073079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.056089 restraints weight = 36222.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057928 restraints weight = 20284.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.059179 restraints weight = 14235.554| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2175 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= 0.111 Angle : 0.510 8.315 16321 Z= 0.256 Chirality : 0.041 0.248 1886 Planarity : 0.003 0.047 2101 Dihedral : 6.851 144.970 1652 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.20 % Allowed : 17.90 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1478 helix: 1.43 (0.23), residues: 510 sheet: -1.58 (0.30), residues: 282 loop : -0.99 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 880 HIS 0.005 0.001 HIS D 973 PHE 0.009 0.001 PHE C 95 TYR 0.022 0.001 TYR D 55 ARG 0.007 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 440) hydrogen bonds : angle 4.52550 ( 1254) covalent geometry : bond 0.00246 (12030) covalent geometry : angle 0.50953 (16321) Misc. bond : bond 0.00109 ( 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 85 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7522 (pp) REVERT: B 192 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8219 (tmtt) REVERT: C 182 TYR cc_start: 0.8627 (m-80) cc_final: 0.8345 (m-80) REVERT: C 190 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7489 (t80) outliers start: 28 outliers final: 23 residues processed: 80 average time/residue: 0.2124 time to fit residues: 27.0811 Evaluate side-chains 77 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 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 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.055212 restraints weight = 36434.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.057054 restraints weight = 21020.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058293 restraints weight = 14853.999| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12034 Z= 0.160 Angle : 0.530 10.493 16321 Z= 0.267 Chirality : 0.042 0.238 1886 Planarity : 0.004 0.046 2101 Dihedral : 6.921 149.172 1652 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.51 % Allowed : 17.66 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1478 helix: 1.45 (0.23), residues: 512 sheet: -1.54 (0.30), residues: 295 loop : -0.98 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 18 HIS 0.006 0.001 HIS D 973 PHE 0.009 0.001 PHE D 95 TYR 0.025 0.002 TYR C 55 ARG 0.005 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 440) hydrogen bonds : angle 4.53968 ( 1254) covalent geometry : bond 0.00361 (12030) covalent geometry : angle 0.53006 (16321) Misc. bond : bond 0.00144 ( 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 85 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7582 (pp) REVERT: B 192 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8317 (tmtt) REVERT: C 182 TYR cc_start: 0.8633 (m-80) cc_final: 0.8342 (m-80) REVERT: C 190 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7514 (t80) REVERT: D 125 LEU cc_start: 0.9017 (mm) cc_final: 0.8814 (mp) outliers start: 32 outliers final: 23 residues processed: 80 average time/residue: 0.1943 time to fit residues: 25.0063 Evaluate side-chains 75 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** 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 = 0.3229 r_free = 0.3229 target = 0.071302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.053905 restraints weight = 36776.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.055678 restraints weight = 21189.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056902 restraints weight = 15077.474| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12034 Z= 0.238 Angle : 0.607 14.033 16321 Z= 0.301 Chirality : 0.044 0.147 1886 Planarity : 0.004 0.046 2101 Dihedral : 7.161 155.492 1652 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.12 % Allowed : 18.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1478 helix: 1.39 (0.23), residues: 512 sheet: -1.69 (0.30), residues: 306 loop : -0.90 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 18 HIS 0.006 0.001 HIS D1016 PHE 0.009 0.001 PHE C 190 TYR 0.028 0.002 TYR C 55 ARG 0.005 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 440) hydrogen bonds : angle 4.68029 ( 1254) covalent geometry : bond 0.00540 (12030) covalent geometry : angle 0.60680 (16321) Misc. bond : bond 0.00191 ( 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 74 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7609 (pp) REVERT: C 190 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7516 (t80) outliers start: 27 outliers final: 24 residues processed: 72 average time/residue: 0.2092 time to fit residues: 24.3762 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 140 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** 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 = 0.3269 r_free = 0.3269 target = 0.073169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055915 restraints weight = 36010.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057753 restraints weight = 20647.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059008 restraints weight = 14603.411| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2260 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= 0.112 Angle : 0.544 15.128 16321 Z= 0.267 Chirality : 0.041 0.145 1886 Planarity : 0.003 0.048 2101 Dihedral : 6.943 149.499 1652 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.73 % Allowed : 18.76 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1478 helix: 1.51 (0.24), residues: 516 sheet: -1.48 (0.30), residues: 293 loop : -0.91 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 880 HIS 0.004 0.001 HIS B 164 PHE 0.009 0.001 PHE C 95 TYR 0.023 0.001 TYR C 55 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 440) hydrogen bonds : angle 4.50478 ( 1254) covalent geometry : bond 0.00248 (12030) covalent geometry : angle 0.54424 (16321) Misc. bond : bond 0.00122 ( 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 78 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 TYR cc_start: 0.8615 (m-80) cc_final: 0.8327 (m-80) REVERT: C 190 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7519 (t80) outliers start: 22 outliers final: 18 residues processed: 75 average time/residue: 0.2151 time to fit residues: 26.2671 Evaluate side-chains 69 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 52 THR 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 1004 LEU Chi-restraints excluded: chain D residue 76 THR 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 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 941 GLN ** 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 = 0.3265 r_free = 0.3265 target = 0.072898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055552 restraints weight = 36022.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057384 restraints weight = 20561.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058616 restraints weight = 14532.495| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12034 Z= 0.128 Angle : 0.546 14.987 16321 Z= 0.268 Chirality : 0.042 0.146 1886 Planarity : 0.003 0.042 2101 Dihedral : 6.912 151.137 1652 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.73 % Allowed : 19.15 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1478 helix: 1.60 (0.23), residues: 515 sheet: -1.47 (0.30), residues: 301 loop : -0.82 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 880 HIS 0.004 0.001 HIS D1016 PHE 0.009 0.001 PHE C 95 TYR 0.026 0.001 TYR D 55 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 440) hydrogen bonds : angle 4.49062 ( 1254) covalent geometry : bond 0.00290 (12030) covalent geometry : angle 0.54646 (16321) Misc. bond : bond 0.00120 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.84 seconds wall clock time: 61 minutes 36.79 seconds (3696.79 seconds total)