Starting phenix.real_space_refine on Mon Oct 26 15:42:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22kk_68398/10_2026/22kk_68398.cif Found real_map, /net/cci-nas-00/data/ceres_data/22kk_68398/10_2026/22kk_68398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22kk_68398/10_2026/22kk_68398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22kk_68398/10_2026/22kk_68398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22kk_68398/10_2026/22kk_68398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22kk_68398/10_2026/22kk_68398.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 13281 2.51 5 N 3566 2.21 5 O 3861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20798 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3515 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 423} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3570 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 422} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3521 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 423} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3581 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 422} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1574 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 190} Chain: "H" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1735 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1567 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 190} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1735 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.63, per 1000 atoms: 0.22 Number of scatterers: 20798 At special positions: 0 Unit cell: (112.039, 187.45, 251.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3861 8.00 N 3566 7.00 C 13281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS C 244 " distance=2.04 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS C 415 " distance=2.04 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS D 244 " distance=2.04 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS D 415 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 206 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 111 " distance=2.03 Simple disulfide: pdb=" SG CYS G 157 " - pdb=" SG CYS G 208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 113 " distance=2.04 Simple disulfide: pdb=" SG CYS H 165 " - pdb=" SG CYS H 221 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 111 " distance=2.04 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 113 " distance=2.04 Simple disulfide: pdb=" SG CYS J 165 " - pdb=" SG CYS J 221 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 932.9 milliseconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4868 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 50 sheets defined 13.5% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.905A pdb=" N ARG B 82 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.692A pdb=" N ILE B 109 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 228 Processing helix chain 'B' and resid 231 through 274 removed outlier: 3.525A pdb=" N LEU B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.562A pdb=" N LEU B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 234 through 286 removed outlier: 3.754A pdb=" N LYS C 238 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 372 through 375 Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.079A pdb=" N ARG A 82 " --> pdb=" O PRO A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.513A pdb=" N GLY A 95 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.622A pdb=" N ILE A 109 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.586A pdb=" N PHE A 227 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 228 " --> pdb=" O GLU A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 228' Processing helix chain 'A' and resid 231 through 273 removed outlier: 4.433A pdb=" N SER A 237 " --> pdb=" O TRP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'D' and resid 74 through 77 removed outlier: 3.501A pdb=" N GLN D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'D' and resid 92 through 95 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.678A pdb=" N ALA D 109 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 285 removed outlier: 3.611A pdb=" N ARG D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.646A pdb=" N ASP G 105 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 106' Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.513A pdb=" N SER H 108 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 159 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 228 through 232 Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 151 through 158 Processing helix chain 'J' and resid 213 through 215 No H-bonds generated for 'chain 'J' and resid 213 through 215' Processing helix chain 'J' and resid 228 through 232 removed outlier: 3.663A pdb=" N GLY J 231 " --> pdb=" O ASN J 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 31 removed outlier: 6.332A pdb=" N VAL B 28 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 132 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 30 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 110 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 53 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 66 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE B 55 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 146 removed outlier: 5.495A pdb=" N TYR B 189 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 192 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.598A pdb=" N TRP C 167 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 175 removed outlier: 4.631A pdb=" N TRP B 167 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ILE C 140 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LYS B 220 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ILE C 142 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU B 222 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLY C 144 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN C 151 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR C 145 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP C 149 " --> pdb=" O TYR C 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 331 removed outlier: 6.051A pdb=" N VAL B 379 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR B 390 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 427 through 432 removed outlier: 6.657A pdb=" N PHE B 420 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR B 431 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 418 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 20 through 22 removed outlier: 7.579A pdb=" N ARG C 96 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP C 90 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.164A pdb=" N VAL C 28 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER C 132 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA C 30 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 301 through 304 removed outlier: 6.256A pdb=" N ILE C 418 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 431 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE C 420 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AB4, first strand: chain 'C' and resid 387 through 391 Processing sheet with id=AB5, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AB6, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.516A pdb=" N ALA A 132 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 110 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 53 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 66 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE A 55 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 178 through 179 removed outlier: 5.985A pdb=" N TYR A 189 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 145 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 151 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 140 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 164 through 168 removed outlier: 9.657A pdb=" N ILE D 140 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS A 220 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE D 142 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 222 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY D 144 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 143 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN D 151 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR D 145 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP D 149 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE D 189 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP D 178 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AC1, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.738A pdb=" N TRP A 353 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 382 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL A 379 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR A 390 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 387 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 340 through 346 removed outlier: 5.717A pdb=" N ASN A 422 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 428 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 20 through 22 removed outlier: 7.537A pdb=" N ARG D 96 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP D 90 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.373A pdb=" N ARG D 57 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D 63 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 301 through 304 removed outlier: 5.529A pdb=" N ASN D 422 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU D 428 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 329 through 331 removed outlier: 7.598A pdb=" N VAL D 379 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N THR D 390 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG D 381 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D 388 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AC8, first strand: chain 'G' and resid 30 through 34 removed outlier: 5.275A pdb=" N TYR G 53 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE G 54 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG G 70 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP G 56 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 30 through 34 Processing sheet with id=AD1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AD2, first strand: chain 'G' and resid 145 through 151 removed outlier: 6.661A pdb=" N TYR G 192 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR G 178 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 145 through 151 removed outlier: 6.661A pdb=" N TYR G 192 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 168 through 172 removed outlier: 3.833A pdb=" N THR G 207 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 27 through 32 removed outlier: 6.579A pdb=" N LYS H 27 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL H 131 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL H 29 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR H 133 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG H 31 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP H 116 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR H 50 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE H 51 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR H 67 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TRP H 53 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 27 through 32 removed outlier: 6.579A pdb=" N LYS H 27 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL H 131 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL H 29 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR H 133 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG H 31 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 37 through 40 Processing sheet with id=AD8, first strand: chain 'H' and resid 144 through 148 removed outlier: 5.492A pdb=" N TYR H 202 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 144 through 148 removed outlier: 5.492A pdb=" N TYR H 202 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 175 through 181 Processing sheet with id=AE2, first strand: chain 'I' and resid 24 through 25 Processing sheet with id=AE3, first strand: chain 'I' and resid 30 through 34 removed outlier: 3.621A pdb=" N GLU I 135 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR I 53 " --> pdb=" O GLY I 114 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE I 54 " --> pdb=" O ARG I 70 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG I 70 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP I 56 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 30 through 34 removed outlier: 3.621A pdb=" N GLU I 135 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 39 through 41 Processing sheet with id=AE6, first strand: chain 'I' and resid 145 through 151 removed outlier: 6.235A pdb=" N TYR I 192 " --> pdb=" O GLU I 161 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR I 178 " --> pdb=" O LYS I 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 145 through 151 removed outlier: 6.235A pdb=" N TYR I 192 " --> pdb=" O GLU I 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 168 through 172 removed outlier: 3.956A pdb=" N THR I 207 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 27 through 32 removed outlier: 6.537A pdb=" N LYS J 27 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL J 131 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL J 29 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR J 133 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG J 31 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP J 116 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR J 50 " --> pdb=" O TRP J 116 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE J 51 " --> pdb=" O TYR J 67 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR J 67 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TRP J 53 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 27 through 32 removed outlier: 6.537A pdb=" N LYS J 27 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL J 131 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL J 29 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR J 133 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG J 31 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 36 through 40 Processing sheet with id=AF3, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.757A pdb=" N TYR J 202 " --> pdb=" O LYS J 169 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.757A pdb=" N TYR J 202 " --> pdb=" O LYS J 169 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 184 through 188 removed outlier: 6.224A pdb=" N THR J 186 " --> pdb=" O GLU J 181 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU J 181 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRP J 179 " --> pdb=" O LEU J 188 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2478 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: 3.64 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6725 1.34 - 1.46: 5222 1.46 - 1.58: 9256 1.58 - 1.71: 4 1.71 - 1.83: 122 Bond restraints: 21329 Sorted by residual: bond pdb=" CB PRO G 182 " pdb=" CG PRO G 182 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.02e+01 bond pdb=" CB PRO D 315 " pdb=" CG PRO D 315 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.14e+00 bond pdb=" CB PRO A 294 " pdb=" CG PRO A 294 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.62e+00 bond pdb=" CB PRO A 319 " pdb=" CG PRO A 319 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" CG PRO A 319 " pdb=" CD PRO A 319 " ideal model delta sigma weight residual 1.503 1.568 -0.065 3.40e-02 8.65e+02 3.66e+00 ... (remaining 21324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 28446 2.80 - 5.60: 424 5.60 - 8.40: 53 8.40 - 11.20: 11 11.20 - 14.00: 4 Bond angle restraints: 28938 Sorted by residual: angle pdb=" CA PRO G 182 " pdb=" N PRO G 182 " pdb=" CD PRO G 182 " ideal model delta sigma weight residual 112.00 98.00 14.00 1.40e+00 5.10e-01 1.00e+02 angle pdb=" CA PRO D 315 " pdb=" N PRO D 315 " pdb=" CD PRO D 315 " ideal model delta sigma weight residual 112.00 101.10 10.90 1.40e+00 5.10e-01 6.07e+01 angle pdb=" CA PRO A 294 " pdb=" N PRO A 294 " pdb=" CD PRO A 294 " ideal model delta sigma weight residual 112.00 103.99 8.01 1.40e+00 5.10e-01 3.27e+01 angle pdb=" C PHE D 228 " pdb=" N GLU D 229 " pdb=" CA GLU D 229 " ideal model delta sigma weight residual 120.67 127.51 -6.84 1.34e+00 5.57e-01 2.60e+01 angle pdb=" N ILE I 177 " pdb=" CA ILE I 177 " pdb=" C ILE I 177 " ideal model delta sigma weight residual 111.62 107.77 3.85 7.90e-01 1.60e+00 2.38e+01 ... (remaining 28933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11019 18.00 - 36.00: 1284 36.00 - 53.99: 321 53.99 - 71.99: 53 71.99 - 89.99: 19 Dihedral angle restraints: 12696 sinusoidal: 5111 harmonic: 7585 Sorted by residual: dihedral pdb=" CB CYS B 461 " pdb=" SG CYS B 461 " pdb=" SG CYS C 415 " pdb=" CB CYS C 415 " ideal model delta sinusoidal sigma weight residual 93.00 173.81 -80.81 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CA CYS A 461 " pdb=" C CYS A 461 " pdb=" N PRO A 462 " pdb=" CA PRO A 462 " ideal model delta harmonic sigma weight residual 180.00 146.40 33.60 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA TYR J 163 " pdb=" C TYR J 163 " pdb=" N LEU J 164 " pdb=" CA LEU J 164 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 12693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2486 0.056 - 0.111: 561 0.111 - 0.167: 101 0.167 - 0.223: 3 0.223 - 0.279: 1 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CB THR H 88 " pdb=" CA THR H 88 " pdb=" OG1 THR H 88 " pdb=" CG2 THR H 88 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA CYS B 244 " pdb=" N CYS B 244 " pdb=" C CYS B 244 " pdb=" CB CYS B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA CYS C 244 " pdb=" N CYS C 244 " pdb=" C CYS C 244 " pdb=" CB CYS C 244 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 3149 not shown) Planarity restraints: 3711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 181 " -0.096 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO G 182 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO G 182 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 182 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 293 " 0.080 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 294 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 461 " -0.055 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 462 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 462 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 462 " -0.045 5.00e-02 4.00e+02 ... (remaining 3708 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1701 2.74 - 3.28: 20620 3.28 - 3.82: 34688 3.82 - 4.36: 40116 4.36 - 4.90: 69370 Nonbonded interactions: 166495 Sorted by model distance: nonbonded pdb=" OE1 GLU A 124 " pdb=" OH TYR H 89 " model vdw 2.197 3.040 nonbonded pdb=" O PRO A 462 " pdb=" N SER A 464 " model vdw 2.201 3.120 nonbonded pdb=" ND2 ASN B 424 " pdb=" O THR C 431 " model vdw 2.204 3.120 nonbonded pdb=" OG SER H 190 " pdb=" OE2 GLU H 192 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 326 " pdb=" O ARG B 364 " model vdw 2.208 3.040 ... (remaining 166490 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 18 through 144 or (resid 145 and (name N or name CA or nam \ e C or name O or name CB )) or resid 146 through 453 or (resid 454 and (name N o \ r name CA or name C or name O or name CB )) or resid 455 through 464)) selection = (chain 'B' and (resid 18 through 325 or (resid 326 and (name N or name CA or nam \ e C or name O or name CB )) or resid 327 through 450 or (resid 451 and (name N o \ r name CA or name C or name O or name CB )) or resid 452 through 464)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 17 through 147 or (resid 148 and (name N or name CA or nam \ e C or name O or name CB )) or resid 149 through 303 or (resid 304 and (name N o \ r name CA or name C or name O or name CB )) or resid 305 through 413 or (resid 4 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 462)) } ncs_group { reference = (chain 'G' and (resid 23 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 119 or (resid 120 and (name N or n \ ame CA or name C or name O or name CB )) or resid 121 through 222)) selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 26 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 134 or (resid 135 and (name N or n \ ame CA or name C or name O or name CB )) or resid 136 through 243)) selection = (chain 'J' and (resid 26 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 92 or (resid 93 through 94 and (na \ me N or name CA or name C or name O or name CB )) or resid 95 through 243)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.460 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.470 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 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 : 0.004 0.159 21349 Z= 0.180 Angle : 0.847 14.001 28978 Z= 0.460 Chirality : 0.048 0.279 3152 Planarity : 0.006 0.135 3711 Dihedral : 16.317 89.988 7768 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.21 % Rotamer: Outliers : 0.53 % Allowed : 27.32 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2606 helix: 1.14 (0.33), residues: 214 sheet: 0.32 (0.16), residues: 1081 loop : -1.01 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 180 TYR 0.030 0.002 TYR J 163 PHE 0.028 0.002 PHE A 391 TRP 0.050 0.002 TRP D 159 HIS 0.006 0.001 HIS G 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (21329) covalent geometry : angle 0.84568 / 0.46 (28938) SS BOND : bond 0.00530 / 0.27 ( 20) SS BOND : angle 1.36535 / 0.90 ( 40) hydrogen bonds : bond 0.11859 / 7.55 ( 887) hydrogen bonds : angle 6.82654 / 4.65 ( 2478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 MET cc_start: 0.2239 (mtt) cc_final: 0.1954 (mtm) REVERT: D 365 ARG cc_start: 0.7041 (mmp80) cc_final: 0.6756 (mmp-170) REVERT: J 173 ASP cc_start: 0.8611 (m-30) cc_final: 0.7671 (p0) outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 0.1717 time to fit residues: 36.4347 Evaluate side-chains 81 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain J residue 141 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 229 GLN B 286 HIS B 316 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 ASN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN H 219 HIS H 228 ASN I 102 GLN ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.078076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.039558 restraints weight = 145355.847| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 7.13 r_work: 0.3022 rms_B_bonded: 6.36 restraints_weight: 2.0000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21349 Z= 0.243 Angle : 0.743 13.180 28978 Z= 0.383 Chirality : 0.048 0.207 3152 Planarity : 0.006 0.078 3711 Dihedral : 5.601 61.922 2863 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.79 % Favored : 93.98 % Rotamer: Outliers : 4.04 % Allowed : 22.92 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2606 helix: 1.23 (0.33), residues: 208 sheet: 0.29 (0.16), residues: 1099 loop : -0.97 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 312 TYR 0.034 0.002 TYR J 163 PHE 0.030 0.002 PHE C 257 TRP 0.038 0.002 TRP C 263 HIS 0.007 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (21329) covalent geometry : angle 0.74208 / 0.38 (28938) SS BOND : bond 0.00498 / 0.28 ( 20) SS BOND : angle 1.38939 / 0.92 ( 40) hydrogen bonds : bond 0.04191 / 2.70 ( 887) hydrogen bonds : angle 5.96914 / 4.12 ( 2478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 74 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.6053 (t0) REVERT: C 51 MET cc_start: 0.3464 (mtt) cc_final: 0.3140 (mtm) REVERT: A 418 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7482 (mt) REVERT: D 51 MET cc_start: 0.4464 (mtm) cc_final: 0.4200 (ptp) REVERT: D 55 PHE cc_start: -0.1108 (OUTLIER) cc_final: -0.1560 (t80) REVERT: D 208 MET cc_start: 0.9377 (tpp) cc_final: 0.8901 (tpp) REVERT: D 275 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7571 (m-70) REVERT: D 365 ARG cc_start: 0.8763 (mmp80) cc_final: 0.8545 (mmp80) REVERT: H 89 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6979 (m-10) REVERT: I 33 MET cc_start: 0.8773 (ttt) cc_final: 0.8320 (ttt) REVERT: J 205 PHE cc_start: 0.4415 (OUTLIER) cc_final: 0.3970 (p90) outliers start: 92 outliers final: 24 residues processed: 163 average time/residue: 0.1506 time to fit residues: 38.5017 Evaluate side-chains 94 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 163 TYR Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [155, 243, 82, 233, 166, 242, 113, 111, 90, 56, 257] chunk 155 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 257 optimal weight: 40.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 229 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN A 215 HIS ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN J 32 GLN ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.064466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.045569 restraints weight = 184191.618| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 5.40 r_work: 0.3041 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21349 Z= 0.241 Angle : 0.692 14.424 28978 Z= 0.357 Chirality : 0.047 0.231 3152 Planarity : 0.005 0.060 3711 Dihedral : 5.232 53.515 2851 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 3.56 % Allowed : 23.14 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2606 helix: 1.20 (0.32), residues: 212 sheet: 0.24 (0.15), residues: 1098 loop : -0.99 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 272 TYR 0.032 0.002 TYR J 163 PHE 0.027 0.002 PHE B 336 TRP 0.026 0.002 TRP D 159 HIS 0.008 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (21329) covalent geometry : angle 0.69004 / 0.36 (28938) SS BOND : bond 0.00653 / 0.44 ( 20) SS BOND : angle 1.40882 / 0.93 ( 40) hydrogen bonds : bond 0.04076 / 2.60 ( 887) hydrogen bonds : angle 5.82125 / 4.03 ( 2478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 65 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 CYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6625 (p) REVERT: B 291 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8910 (t) REVERT: B 391 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: B 424 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6696 (t160) REVERT: C 51 MET cc_start: 0.3005 (mtt) cc_final: 0.2674 (mtm) REVERT: C 237 THR cc_start: 0.2209 (OUTLIER) cc_final: 0.1823 (m) REVERT: A 391 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: A 461 CYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6339 (p) REVERT: D 55 PHE cc_start: -0.1808 (OUTLIER) cc_final: -0.2158 (t80) REVERT: D 208 MET cc_start: 0.9405 (tpp) cc_final: 0.9037 (tpp) REVERT: D 275 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7681 (m-70) REVERT: D 368 TYR cc_start: 0.7972 (t80) cc_final: 0.7682 (t80) REVERT: D 407 ILE cc_start: 0.9319 (mm) cc_final: 0.8883 (mp) REVERT: H 89 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6415 (m-10) REVERT: I 33 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8414 (tpt) REVERT: I 155 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7429 (m) REVERT: J 205 PHE cc_start: 0.4814 (OUTLIER) cc_final: 0.4372 (p90) outliers start: 81 outliers final: 30 residues processed: 142 average time/residue: 0.1380 time to fit residues: 31.9554 Evaluate side-chains 105 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain G residue 222 PHE Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [217, 4, 87, 82, 174, 153, 163, 149, 106, 102, 95] chunk 217 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 182 ASN B 229 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 341 HIS A 424 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.076569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.040863 restraints weight = 146250.126| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 8.39 r_work: 0.2952 rms_B_bonded: 6.68 restraints_weight: 2.0000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21349 Z= 0.182 Angle : 0.650 16.799 28978 Z= 0.332 Chirality : 0.046 0.205 3152 Planarity : 0.005 0.060 3711 Dihedral : 5.026 59.468 2847 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 3.16 % Allowed : 22.88 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2606 helix: 1.27 (0.33), residues: 212 sheet: 0.21 (0.15), residues: 1126 loop : -0.90 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 183 TYR 0.020 0.001 TYR J 163 PHE 0.023 0.002 PHE B 391 TRP 0.047 0.001 TRP C 263 HIS 0.008 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (21329) covalent geometry : angle 0.64782 / 0.33 (28938) SS BOND : bond 0.00388 / 0.21 ( 20) SS BOND : angle 1.42606 / 0.99 ( 40) hydrogen bonds : bond 0.03776 / 2.41 ( 887) hydrogen bonds : angle 5.64489 / 3.92 ( 2478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 63 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 381 ARG cc_start: 0.9553 (OUTLIER) cc_final: 0.9003 (tmm-80) REVERT: B 391 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: B 424 ASN cc_start: 0.7011 (OUTLIER) cc_final: 0.6512 (t0) REVERT: C 51 MET cc_start: 0.3933 (mtt) cc_final: 0.3719 (mtm) REVERT: C 237 THR cc_start: 0.2290 (OUTLIER) cc_final: 0.1830 (m) REVERT: A 124 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: A 391 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8772 (m-80) REVERT: D 55 PHE cc_start: -0.1489 (OUTLIER) cc_final: -0.1955 (t80) REVERT: D 208 MET cc_start: 0.9457 (tpp) cc_final: 0.9042 (tpp) REVERT: D 407 ILE cc_start: 0.9430 (mm) cc_final: 0.9051 (mp) REVERT: H 89 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6161 (m-10) REVERT: I 33 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: J 205 PHE cc_start: 0.4494 (OUTLIER) cc_final: 0.4093 (p90) outliers start: 72 outliers final: 39 residues processed: 131 average time/residue: 0.1395 time to fit residues: 29.5249 Evaluate side-chains 111 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 62 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [199, 227, 173, 52, 210, 226, 41, 15, 175, 123, 91] chunk 199 optimal weight: 0.1980 chunk 227 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 15 optimal weight: 0.0970 chunk 175 optimal weight: 40.0000 chunk 123 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 229 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.064718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.044239 restraints weight = 182445.864| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 5.56 r_work: 0.3104 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21349 Z= 0.118 Angle : 0.625 18.573 28978 Z= 0.314 Chirality : 0.046 0.216 3152 Planarity : 0.004 0.061 3711 Dihedral : 4.824 59.270 2847 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.72 % Favored : 95.13 % Rotamer: Outliers : 2.64 % Allowed : 23.14 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2606 helix: 1.40 (0.33), residues: 212 sheet: 0.36 (0.15), residues: 1123 loop : -0.84 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.019 0.001 TYR J 119 PHE 0.022 0.001 PHE B 391 TRP 0.029 0.001 TRP C 263 HIS 0.008 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21329) covalent geometry : angle 0.62361 / 0.31 (28938) SS BOND : bond 0.00413 / 0.23 ( 20) SS BOND : angle 1.32655 / 0.91 ( 40) hydrogen bonds : bond 0.03539 / 2.28 ( 887) hydrogen bonds : angle 5.42987 / 3.78 ( 2478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 63 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: B 381 ARG cc_start: 0.9495 (OUTLIER) cc_final: 0.8892 (tmm-80) REVERT: B 391 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: B 424 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6592 (t0) REVERT: C 51 MET cc_start: 0.3392 (mtt) cc_final: 0.3040 (ptp) REVERT: A 124 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: A 391 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: D 55 PHE cc_start: -0.1656 (OUTLIER) cc_final: -0.2082 (t80) REVERT: D 208 MET cc_start: 0.9408 (tpp) cc_final: 0.9081 (tpp) REVERT: D 275 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7390 (m-70) REVERT: D 407 ILE cc_start: 0.9289 (mm) cc_final: 0.8849 (mp) REVERT: I 33 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8320 (tpt) REVERT: J 205 PHE cc_start: 0.4852 (OUTLIER) cc_final: 0.4371 (p90) outliers start: 60 outliers final: 30 residues processed: 120 average time/residue: 0.1314 time to fit residues: 25.7161 Evaluate side-chains 101 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 61 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [110, 26, 102, 230, 137, 246, 25, 84, 62, 156, 227] chunk 110 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 102 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 246 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 62 optimal weight: 0.0470 chunk 156 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.064927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.047664 restraints weight = 180977.874| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 6.31 r_work: 0.3092 rms_B_bonded: 6.11 restraints_weight: 2.0000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21349 Z= 0.107 Angle : 0.620 20.823 28978 Z= 0.310 Chirality : 0.046 0.194 3152 Planarity : 0.004 0.061 3711 Dihedral : 4.694 58.933 2847 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 2.55 % Allowed : 23.32 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2606 helix: 1.39 (0.33), residues: 212 sheet: 0.46 (0.16), residues: 1125 loop : -0.80 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 354 TYR 0.019 0.001 TYR J 119 PHE 0.021 0.001 PHE B 391 TRP 0.065 0.001 TRP C 263 HIS 0.008 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (21329) covalent geometry : angle 0.61869 / 0.31 (28938) SS BOND : bond 0.00393 / 0.21 ( 20) SS BOND : angle 1.24533 / 0.84 ( 40) hydrogen bonds : bond 0.03418 / 2.21 ( 887) hydrogen bonds : angle 5.30249 / 3.70 ( 2478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 60 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: B 192 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: B 381 ARG cc_start: 0.9466 (OUTLIER) cc_final: 0.8920 (tmm-80) REVERT: B 418 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.8833 (tp) REVERT: B 420 PHE cc_start: 0.9091 (m-80) cc_final: 0.8430 (m-80) REVERT: B 424 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.6811 (t0) REVERT: C 51 MET cc_start: 0.3063 (mtt) cc_final: 0.2743 (ptp) REVERT: A 124 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 391 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: A 461 CYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6400 (p) REVERT: D 55 PHE cc_start: -0.1939 (OUTLIER) cc_final: -0.2276 (t80) REVERT: D 208 MET cc_start: 0.9453 (tpp) cc_final: 0.9129 (tpp) REVERT: D 275 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7177 (m-70) REVERT: D 407 ILE cc_start: 0.9215 (mm) cc_final: 0.8741 (mp) REVERT: I 33 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8401 (tpt) REVERT: I 155 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7351 (m) REVERT: J 205 PHE cc_start: 0.4910 (OUTLIER) cc_final: 0.4409 (p90) outliers start: 58 outliers final: 34 residues processed: 115 average time/residue: 0.1429 time to fit residues: 26.8443 Evaluate side-chains 107 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [107, 190, 101, 116, 92, 105, 45, 209, 29, 187, 142] chunk 107 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 209 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 HIS ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS A 350 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.073298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.040910 restraints weight = 153775.931| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 8.54 r_work: 0.2926 rms_B_bonded: 6.36 restraints_weight: 2.0000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21349 Z= 0.269 Angle : 0.688 18.604 28978 Z= 0.351 Chirality : 0.047 0.193 3152 Planarity : 0.005 0.060 3711 Dihedral : 5.007 44.774 2847 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.68 % Favored : 94.17 % Rotamer: Outliers : 3.29 % Allowed : 22.66 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2606 helix: 1.32 (0.33), residues: 212 sheet: 0.22 (0.15), residues: 1134 loop : -0.91 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 401 TYR 0.019 0.002 TYR B 189 PHE 0.022 0.002 PHE A 391 TRP 0.050 0.002 TRP C 263 HIS 0.008 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 (21329) covalent geometry : angle 0.68628 / 0.35 (28938) SS BOND : bond 0.00503 / 0.30 ( 20) SS BOND : angle 1.60600 / 1.10 ( 40) hydrogen bonds : bond 0.03917 / 2.50 ( 887) hydrogen bonds : angle 5.63165 / 3.94 ( 2478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 61 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: B 381 ARG cc_start: 0.9503 (OUTLIER) cc_final: 0.8939 (tmm-80) REVERT: B 424 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6976 (t160) REVERT: C 51 MET cc_start: 0.3656 (mtt) cc_final: 0.3414 (mtm) REVERT: A 289 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: D 55 PHE cc_start: -0.1444 (OUTLIER) cc_final: -0.1949 (t80) REVERT: D 208 MET cc_start: 0.9430 (tpp) cc_final: 0.9171 (tpp) REVERT: D 275 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7959 (m-70) REVERT: D 368 TYR cc_start: 0.7926 (t80) cc_final: 0.7596 (t80) REVERT: H 89 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: I 33 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8301 (tpt) REVERT: I 155 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7941 (m) outliers start: 75 outliers final: 48 residues processed: 133 average time/residue: 0.1348 time to fit residues: 29.4055 Evaluate side-chains 114 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 57 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 222 PHE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 202 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [124, 151, 64, 7, 75, 104, 98, 165, 180, 102, 73] chunk 124 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** 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 = 0.4192 r_free = 0.4192 target = 0.063529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.044931 restraints weight = 182153.691| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.27 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21349 Z= 0.196 Angle : 0.654 18.931 28978 Z= 0.330 Chirality : 0.046 0.215 3152 Planarity : 0.005 0.060 3711 Dihedral : 4.832 28.226 2845 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 2.68 % Allowed : 23.14 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2606 helix: 1.20 (0.33), residues: 214 sheet: 0.20 (0.15), residues: 1131 loop : -0.89 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.023 0.001 TYR D 443 PHE 0.019 0.002 PHE B 391 TRP 0.043 0.002 TRP C 263 HIS 0.004 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (21329) covalent geometry : angle 0.65243 / 0.33 (28938) SS BOND : bond 0.00406 / 0.22 ( 20) SS BOND : angle 1.54281 / 1.05 ( 40) hydrogen bonds : bond 0.03682 / 2.34 ( 887) hydrogen bonds : angle 5.54316 / 3.89 ( 2478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 59 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: B 381 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8805 (tmm-80) REVERT: B 418 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 420 PHE cc_start: 0.8552 (m-80) cc_final: 0.7997 (m-80) REVERT: B 424 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6657 (t160) REVERT: A 124 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: D 55 PHE cc_start: -0.2957 (OUTLIER) cc_final: -0.3230 (t80) REVERT: D 275 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7901 (m-70) REVERT: D 368 TYR cc_start: 0.7306 (t80) cc_final: 0.7009 (t80) REVERT: D 407 ILE cc_start: 0.8985 (mm) cc_final: 0.8455 (mp) REVERT: H 168 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: I 33 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8047 (tpt) REVERT: I 155 VAL cc_start: 0.6933 (OUTLIER) cc_final: 0.6696 (m) REVERT: J 205 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5666 (p90) outliers start: 61 outliers final: 42 residues processed: 117 average time/residue: 0.1365 time to fit residues: 26.2959 Evaluate side-chains 112 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 59 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 202 TYR Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [148, 52, 18, 121, 222, 198, 174, 87, 31, 181, 128] chunk 148 optimal weight: 9.9990 chunk 52 optimal weight: 40.0000 chunk 18 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 198 optimal weight: 0.0030 chunk 174 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 31 optimal weight: 40.0000 chunk 181 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 392 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.062178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.043596 restraints weight = 182635.066| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.28 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 21349 Z= 0.413 Angle : 0.805 16.595 28978 Z= 0.412 Chirality : 0.049 0.197 3152 Planarity : 0.005 0.059 3711 Dihedral : 5.433 34.603 2845 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.75 % Favored : 93.05 % Rotamer: Outliers : 2.81 % Allowed : 23.45 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2606 helix: 0.97 (0.32), residues: 214 sheet: -0.12 (0.15), residues: 1093 loop : -1.10 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 162 TYR 0.024 0.003 TYR D 443 PHE 0.031 0.003 PHE B 391 TRP 0.041 0.003 TRP C 263 HIS 0.009 0.002 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.41 (21329) covalent geometry : angle 0.80215 / 0.41 (28938) SS BOND : bond 0.00664 / 0.40 ( 20) SS BOND : angle 1.99168 / 1.35 ( 40) hydrogen bonds : bond 0.04476 / 2.84 ( 887) hydrogen bonds : angle 6.10154 / 4.30 ( 2478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 60 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: B 381 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.8763 (tmm-80) REVERT: B 418 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.8730 (tp) REVERT: B 420 PHE cc_start: 0.8798 (m-80) cc_final: 0.8136 (m-80) REVERT: B 424 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.6716 (t160) REVERT: C 185 MET cc_start: 0.9100 (pmm) cc_final: 0.8877 (pmm) REVERT: D 55 PHE cc_start: -0.2468 (OUTLIER) cc_final: -0.2895 (t80) REVERT: D 275 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7922 (m-70) REVERT: H 89 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: H 168 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: I 33 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8104 (tpt) REVERT: I 155 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7085 (m) REVERT: J 205 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5638 (p90) outliers start: 64 outliers final: 47 residues processed: 120 average time/residue: 0.1410 time to fit residues: 27.5838 Evaluate side-chains 116 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 58 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 202 TYR Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [66, 144, 189, 177, 122, 74, 199, 161, 39, 0, 178] chunk 66 optimal weight: 40.0000 chunk 144 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 122 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 0 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** 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 = 0.4158 r_free = 0.4158 target = 0.062346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.043826 restraints weight = 185249.904| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 5.59 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.288 21349 Z= 0.307 Angle : 0.913 59.200 28978 Z= 0.495 Chirality : 0.047 0.202 3152 Planarity : 0.005 0.059 3711 Dihedral : 5.457 34.523 2845 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.60 % Favored : 93.21 % Rotamer: Outliers : 2.77 % Allowed : 23.45 % Favored : 73.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2606 helix: 0.97 (0.32), residues: 214 sheet: -0.16 (0.15), residues: 1093 loop : -1.11 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 180 TYR 0.021 0.002 TYR H 202 PHE 0.032 0.002 PHE B 391 TRP 0.047 0.003 TRP C 263 HIS 0.006 0.001 HIS D 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.31 (21329) covalent geometry : angle 0.91078 / 0.49 (28938) SS BOND : bond 0.00674 / 0.40 ( 20) SS BOND : angle 1.89027 / 1.26 ( 40) hydrogen bonds : bond 0.04330 / 2.74 ( 887) hydrogen bonds : angle 6.10486 / 4.30 ( 2478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 58 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: B 381 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8765 (tmm-80) REVERT: B 418 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.8734 (tp) REVERT: B 420 PHE cc_start: 0.8747 (m-80) cc_final: 0.8138 (m-80) REVERT: B 424 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6714 (t160) REVERT: C 185 MET cc_start: 0.9090 (pmm) cc_final: 0.8864 (pmm) REVERT: D 55 PHE cc_start: -0.2443 (OUTLIER) cc_final: -0.2826 (t80) REVERT: D 275 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7912 (m-70) REVERT: H 89 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: H 168 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: I 33 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8102 (tpt) REVERT: I 155 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7207 (m) REVERT: J 205 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5507 (p90) outliers start: 63 outliers final: 49 residues processed: 119 average time/residue: 0.1431 time to fit residues: 27.7953 Evaluate side-chains 117 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 57 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 263 TRP Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 222 PHE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 202 TYR Chi-restraints excluded: chain J residue 205 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [146, 163, 123, 6, 203, 161, 238, 190, 241, 21, 137] chunk 146 optimal weight: 1.9990 chunk 163 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 203 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 241 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 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 = 0.4158 r_free = 0.4158 target = 0.062358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.043681 restraints weight = 184770.403| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.59 r_work: 0.2958 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.288 21349 Z= 0.307 Angle : 0.913 59.200 28978 Z= 0.495 Chirality : 0.047 0.202 3152 Planarity : 0.005 0.059 3711 Dihedral : 5.457 34.523 2845 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.60 % Favored : 93.21 % Rotamer: Outliers : 2.64 % Allowed : 23.54 % Favored : 73.83 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2606 helix: 0.97 (0.32), residues: 214 sheet: -0.16 (0.15), residues: 1093 loop : -1.11 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 180 TYR 0.021 0.002 TYR H 202 PHE 0.032 0.002 PHE B 391 TRP 0.047 0.003 TRP C 263 HIS 0.006 0.001 HIS D 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.31 (21329) covalent geometry : angle 0.91078 / 0.49 (28938) SS BOND : bond 0.00674 / 0.40 ( 20) SS BOND : angle 1.89027 / 1.26 ( 40) hydrogen bonds : bond 0.04330 / 2.74 ( 887) hydrogen bonds : angle 6.10486 / 4.30 ( 2478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8848.93 seconds wall clock time: 151 minutes 12.16 seconds (9072.16 seconds total)