Starting phenix.real_space_refine on Sat Oct 11 11:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7h_18973/10_2025/8r7h_18973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7h_18973/10_2025/8r7h_18973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r7h_18973/10_2025/8r7h_18973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7h_18973/10_2025/8r7h_18973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r7h_18973/10_2025/8r7h_18973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7h_18973/10_2025/8r7h_18973.map" } resolution = 3.29 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= 0.001 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 72 5.16 5 C 8994 2.51 5 N 2496 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14258 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3590 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3539 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3539 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3590 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.46, per 1000 atoms: 0.24 Number of scatterers: 14258 At special positions: 0 Unit cell: (132.461, 123.571, 99.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 2 15.00 O 2694 8.00 N 2496 7.00 C 8994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 628.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 16 sheets defined 53.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.632A pdb=" N LEU A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.797A pdb=" N ASN A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.859A pdb=" N TYR A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.527A pdb=" N GLY A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.675A pdb=" N ARG A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.898A pdb=" N GLU A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.717A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 321 through 345 removed outlier: 3.776A pdb=" N LYS A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.674A pdb=" N ALA A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 440 Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 457 through 473 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.579A pdb=" N TYR B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.569A pdb=" N LEU B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.927A pdb=" N ASN B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 71 " --> pdb=" O CYS B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 71' Processing helix chain 'B' and resid 86 through 104 removed outlier: 3.846A pdb=" N TYR B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.880A pdb=" N GLU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.593A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 Processing helix chain 'B' and resid 321 through 345 removed outlier: 3.793A pdb=" N LYS B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.690A pdb=" N SER B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 440 removed outlier: 3.784A pdb=" N LYS B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 454 through 473 removed outlier: 4.350A pdb=" N ALA B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.990A pdb=" N LEU C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.681A pdb=" N TYR C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.508A pdb=" N LEU C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.923A pdb=" N ASN C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.865A pdb=" N TYR C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 161 through 167 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.880A pdb=" N LEU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.897A pdb=" N GLU C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 247' Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.553A pdb=" N LEU C 291 " --> pdb=" O ASN C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 320 Processing helix chain 'C' and resid 321 through 345 removed outlier: 3.791A pdb=" N LYS C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.989A pdb=" N GLY C 352 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.586A pdb=" N ALA C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 414 through 440 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.694A pdb=" N ALA C 453 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 473 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.618A pdb=" N TYR D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.743A pdb=" N ASN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.893A pdb=" N TYR D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.736A pdb=" N ARG D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 222 Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.941A pdb=" N GLU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.716A pdb=" N LEU D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 320 Processing helix chain 'D' and resid 321 through 345 removed outlier: 3.798A pdb=" N LYS D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.774A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 414 through 440 Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 454 through 473 removed outlier: 4.329A pdb=" N ALA D 460 " --> pdb=" O LYS D 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.154A pdb=" N LEU A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 252 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 227 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR A 254 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 198 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP A 228 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 200 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG A 137 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE A 199 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N MET A 139 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 201 " --> pdb=" O MET A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 276 removed outlier: 7.268A pdb=" N ILE A 284 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.910A pdb=" N LYS A 348 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 385 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.175A pdb=" N LEU B 225 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR B 252 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA B 227 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR B 254 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 228 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG B 137 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE B 199 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET B 139 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 201 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 273 through 276 removed outlier: 7.131A pdb=" N ILE B 284 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 removed outlier: 7.050A pdb=" N LEU C 48 " --> pdb=" O ALA C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 77 removed outlier: 4.079A pdb=" N TYR C 77 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.175A pdb=" N LEU C 225 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR C 252 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA C 227 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR C 254 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG C 137 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 199 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET C 139 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY C 201 " --> pdb=" O MET C 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.696A pdb=" N SER C 275 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 362 removed outlier: 4.354A pdb=" N ILE C 359 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 402 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN C 385 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 48 through 49 removed outlier: 7.339A pdb=" N LEU D 48 " --> pdb=" O ALA D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 77 removed outlier: 4.051A pdb=" N TYR D 77 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 111 through 114 removed outlier: 6.254A pdb=" N LEU D 225 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR D 252 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA D 227 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR D 254 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG D 137 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE D 199 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET D 139 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLY D 201 " --> pdb=" O MET D 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 273 through 276 removed outlier: 3.783A pdb=" N SER D 275 " --> pdb=" O ILE D 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 348 through 349 removed outlier: 4.172A pdb=" N LYS D 348 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 385 " --> pdb=" O ARG D 402 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.58 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: 4740 1.34 - 1.46: 1938 1.46 - 1.57: 7756 1.57 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 14540 Sorted by residual: bond pdb=" OP4 LLP D 257 " pdb=" P LLP D 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.23e+01 bond pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C4 LLP D 257 " pdb=" C4' LLP D 257 " ideal model delta sigma weight residual 1.464 1.616 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 14535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19494 2.13 - 4.26: 132 4.26 - 6.39: 39 6.39 - 8.51: 1 8.51 - 10.64: 6 Bond angle restraints: 19672 Sorted by residual: angle pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " pdb=" C4 LLP D 257 " ideal model delta sigma weight residual 120.09 109.45 10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " pdb=" C4 LLP A 257 " ideal model delta sigma weight residual 120.09 109.66 10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CE LLP D 257 " pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " ideal model delta sigma weight residual 119.26 109.39 9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CE LLP A 257 " pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 119.26 109.48 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C HIS C 256 " pdb=" N LYS C 257 " pdb=" CA LYS C 257 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.74e+00 ... (remaining 19667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 8339 16.93 - 33.87: 356 33.87 - 50.80: 49 50.80 - 67.74: 10 67.74 - 84.67: 12 Dihedral angle restraints: 8766 sinusoidal: 3458 harmonic: 5308 Sorted by residual: dihedral pdb=" CA PRO C 134 " pdb=" C PRO C 134 " pdb=" N HIS C 135 " pdb=" CA HIS C 135 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N HIS B 135 " pdb=" CA HIS B 135 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PRO D 134 " pdb=" C PRO D 134 " pdb=" N HIS D 135 " pdb=" CA HIS D 135 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 8763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1433 0.028 - 0.055: 511 0.055 - 0.083: 140 0.083 - 0.110: 81 0.110 - 0.138: 25 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA PRO A 134 " pdb=" N PRO A 134 " pdb=" C PRO A 134 " pdb=" CB PRO A 134 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA PRO D 134 " pdb=" N PRO D 134 " pdb=" C PRO D 134 " pdb=" CB PRO D 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA PRO B 134 " pdb=" N PRO B 134 " pdb=" C PRO B 134 " pdb=" CB PRO B 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2187 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 257 " -0.164 2.00e-02 2.50e+03 2.93e-01 8.56e+02 pdb=" NZ LLP A 257 " 0.400 2.00e-02 2.50e+03 pdb=" C4 LLP A 257 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 257 " -0.371 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP D 257 " 0.162 2.00e-02 2.50e+03 2.81e-01 7.89e+02 pdb=" NZ LLP D 257 " -0.381 2.00e-02 2.50e+03 pdb=" C4 LLP D 257 " -0.135 2.00e-02 2.50e+03 pdb=" C4' LLP D 257 " 0.355 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 116 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 117 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " 0.021 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3548 2.79 - 3.32: 13342 3.32 - 3.84: 23072 3.84 - 4.37: 27388 4.37 - 4.90: 46349 Nonbonded interactions: 113699 Sorted by model distance: nonbonded pdb=" OG SER B 233 " pdb=" OG1 THR B 258 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 119 " pdb=" OP1 LLP A 257 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR C 155 " pdb=" O LYS C 158 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 368 " pdb=" OE1 GLN C 436 " model vdw 2.295 3.040 nonbonded pdb=" O ILE A 429 " pdb=" OG1 THR A 432 " model vdw 2.310 3.040 ... (remaining 113694 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 146 or resid 153 through 256 or resid 258 throu \ gh 480)) selection = (chain 'B' and (resid 16 through 256 or resid 258 through 480)) selection = (chain 'C' and (resid 16 through 256 or resid 258 through 480)) selection = (chain 'D' and (resid 16 through 146 or resid 153 through 256 or resid 258 throu \ gh 480)) } 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 0.181 14540 Z= 0.213 Angle : 0.501 10.642 19672 Z= 0.260 Chirality : 0.036 0.138 2190 Planarity : 0.009 0.293 2566 Dihedral : 9.961 84.671 5378 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.86 % Allowed : 4.43 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: -1.80 (0.17), residues: 1832 helix: -0.15 (0.16), residues: 886 sheet: -1.38 (0.33), residues: 222 loop : -2.42 (0.19), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 451 TYR 0.005 0.000 TYR D 205 PHE 0.005 0.001 PHE D 268 TRP 0.001 0.000 TRP B 111 HIS 0.003 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00421 (14540) covalent geometry : angle 0.50068 (19672) hydrogen bonds : bond 0.14928 ( 716) hydrogen bonds : angle 5.25007 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 263 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8751 (tp30) cc_final: 0.8500 (tp30) REVERT: A 160 ILE cc_start: 0.9290 (mt) cc_final: 0.9053 (mm) REVERT: A 229 MET cc_start: 0.8435 (ptm) cc_final: 0.7881 (ptm) REVERT: A 449 LYS cc_start: 0.8429 (tppt) cc_final: 0.8092 (tppt) REVERT: B 63 GLU cc_start: 0.8725 (tt0) cc_final: 0.8357 (tm-30) REVERT: B 173 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8298 (mmmm) REVERT: C 198 ILE cc_start: 0.8966 (mt) cc_final: 0.8701 (mp) REVERT: C 465 ARG cc_start: 0.9197 (ttm170) cc_final: 0.8949 (mtp-110) REVERT: D 159 LYS cc_start: 0.8952 (mttp) cc_final: 0.8734 (mttm) outliers start: 13 outliers final: 9 residues processed: 276 average time/residue: 0.1553 time to fit residues: 58.8008 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 102 GLN A 109 GLN A 231 HIS A 318 GLN A 357 HIS A 458 GLN B 102 GLN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN C 97 GLN C 102 GLN C 109 GLN C 330 GLN C 458 GLN D 102 GLN D 318 GLN D 458 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055872 restraints weight = 52570.982| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.11 r_work: 0.2813 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14540 Z= 0.117 Angle : 0.525 9.628 19672 Z= 0.263 Chirality : 0.038 0.138 2190 Planarity : 0.004 0.066 2566 Dihedral : 5.327 87.404 2042 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.65 % Allowed : 10.52 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: -0.22 (0.19), residues: 1832 helix: 1.28 (0.17), residues: 902 sheet: -1.08 (0.33), residues: 220 loop : -1.73 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.011 0.001 TYR C 183 PHE 0.014 0.001 PHE A 418 TRP 0.005 0.001 TRP A 111 HIS 0.003 0.001 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00269 (14540) covalent geometry : angle 0.52506 (19672) hydrogen bonds : bond 0.03203 ( 716) hydrogen bonds : angle 3.91790 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9274 (mt) cc_final: 0.9034 (mm) REVERT: A 229 MET cc_start: 0.9131 (ptm) cc_final: 0.8426 (ptm) REVERT: A 384 CYS cc_start: 0.8922 (t) cc_final: 0.8327 (t) REVERT: A 449 LYS cc_start: 0.8564 (tppt) cc_final: 0.8195 (tppt) REVERT: B 21 MET cc_start: 0.9026 (ttp) cc_final: 0.8713 (ttt) REVERT: B 63 GLU cc_start: 0.9097 (tt0) cc_final: 0.8624 (tm-30) REVERT: B 133 GLU cc_start: 0.8832 (tp30) cc_final: 0.8548 (tp30) REVERT: B 173 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8705 (mmmm) REVERT: C 54 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8568 (mm-30) REVERT: C 198 ILE cc_start: 0.9322 (mt) cc_final: 0.9120 (mp) REVERT: C 465 ARG cc_start: 0.9208 (ttm170) cc_final: 0.8993 (mtp-110) REVERT: D 159 LYS cc_start: 0.9025 (mttp) cc_final: 0.8736 (mttm) REVERT: D 229 MET cc_start: 0.9256 (ptm) cc_final: 0.8941 (ptt) REVERT: D 378 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8841 (pp20) outliers start: 25 outliers final: 19 residues processed: 158 average time/residue: 0.1270 time to fit residues: 29.6355 Evaluate side-chains 144 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 24 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053593 restraints weight = 51831.263| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 4.19 r_work: 0.2726 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14540 Z= 0.129 Angle : 0.522 10.124 19672 Z= 0.262 Chirality : 0.039 0.194 2190 Planarity : 0.004 0.063 2566 Dihedral : 5.374 88.291 2041 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.12 % Allowed : 11.71 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.31 (0.19), residues: 1832 helix: 1.78 (0.18), residues: 902 sheet: -0.89 (0.33), residues: 220 loop : -1.54 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.009 0.001 TYR C 224 PHE 0.012 0.001 PHE D 418 TRP 0.002 0.001 TRP A 111 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00300 (14540) covalent geometry : angle 0.52192 (19672) hydrogen bonds : bond 0.03306 ( 716) hydrogen bonds : angle 3.83102 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9374 (mt) cc_final: 0.9148 (mm) REVERT: A 229 MET cc_start: 0.9243 (ptm) cc_final: 0.8372 (ptm) REVERT: A 232 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9015 (pt) REVERT: A 449 LYS cc_start: 0.8572 (tppt) cc_final: 0.8267 (tppt) REVERT: B 21 MET cc_start: 0.9001 (ttp) cc_final: 0.8637 (ttp) REVERT: B 63 GLU cc_start: 0.9052 (tt0) cc_final: 0.8593 (tm-30) REVERT: B 133 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: B 173 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8821 (mmmm) REVERT: C 54 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8568 (mm-30) REVERT: C 465 ARG cc_start: 0.9195 (ttm170) cc_final: 0.8932 (mtp-110) REVERT: D 187 GLU cc_start: 0.9490 (tt0) cc_final: 0.9212 (tm-30) REVERT: D 220 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8966 (tm-30) outliers start: 32 outliers final: 16 residues processed: 147 average time/residue: 0.1246 time to fit residues: 26.9894 Evaluate side-chains 126 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 171 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 165 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054565 restraints weight = 51954.091| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.20 r_work: 0.2750 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14540 Z= 0.091 Angle : 0.489 8.710 19672 Z= 0.245 Chirality : 0.038 0.142 2190 Planarity : 0.004 0.052 2566 Dihedral : 5.308 87.850 2041 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.46 % Allowed : 13.29 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.57 (0.20), residues: 1832 helix: 1.97 (0.18), residues: 902 sheet: -0.66 (0.34), residues: 220 loop : -1.42 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 402 TYR 0.010 0.001 TYR B 83 PHE 0.008 0.001 PHE D 418 TRP 0.002 0.000 TRP C 111 HIS 0.002 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00206 (14540) covalent geometry : angle 0.48885 (19672) hydrogen bonds : bond 0.02803 ( 716) hydrogen bonds : angle 3.69972 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.9228 (tt0) cc_final: 0.9003 (pp20) REVERT: A 160 ILE cc_start: 0.9330 (mt) cc_final: 0.9095 (mm) REVERT: A 229 MET cc_start: 0.9208 (ptm) cc_final: 0.8418 (ptm) REVERT: A 232 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8998 (pt) REVERT: A 384 CYS cc_start: 0.9020 (t) cc_final: 0.8455 (t) REVERT: A 449 LYS cc_start: 0.8597 (tppt) cc_final: 0.8229 (tppt) REVERT: B 21 MET cc_start: 0.8984 (ttp) cc_final: 0.8607 (ttp) REVERT: B 63 GLU cc_start: 0.9004 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 133 GLU cc_start: 0.8890 (tp30) cc_final: 0.8580 (tp30) REVERT: B 173 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8814 (mmmm) REVERT: B 466 GLU cc_start: 0.9359 (pt0) cc_final: 0.9155 (tp30) REVERT: C 54 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8577 (mm-30) REVERT: C 465 ARG cc_start: 0.9178 (ttm170) cc_final: 0.8922 (mtp-110) REVERT: D 220 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8961 (tm-30) REVERT: D 229 MET cc_start: 0.9322 (ptm) cc_final: 0.9039 (ptt) outliers start: 22 outliers final: 13 residues processed: 140 average time/residue: 0.1139 time to fit residues: 24.0169 Evaluate side-chains 125 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 113 optimal weight: 0.0050 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.053302 restraints weight = 51741.841| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.18 r_work: 0.2727 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14540 Z= 0.108 Angle : 0.501 8.156 19672 Z= 0.251 Chirality : 0.038 0.178 2190 Planarity : 0.004 0.054 2566 Dihedral : 5.257 88.180 2040 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.79 % Allowed : 13.36 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.81 (0.20), residues: 1832 helix: 2.20 (0.18), residues: 898 sheet: -0.59 (0.34), residues: 228 loop : -1.32 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.009 0.001 TYR B 83 PHE 0.010 0.001 PHE D 418 TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00250 (14540) covalent geometry : angle 0.50074 (19672) hydrogen bonds : bond 0.02973 ( 716) hydrogen bonds : angle 3.66404 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9225 (mt) cc_final: 0.8979 (mm) REVERT: A 229 MET cc_start: 0.9232 (ptm) cc_final: 0.8402 (ptm) REVERT: A 232 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9019 (pt) REVERT: A 449 LYS cc_start: 0.8594 (tppt) cc_final: 0.8291 (tppt) REVERT: B 21 MET cc_start: 0.9044 (ttp) cc_final: 0.8664 (ttp) REVERT: B 49 GLU cc_start: 0.7697 (mp0) cc_final: 0.7446 (mp0) REVERT: B 63 GLU cc_start: 0.8973 (tt0) cc_final: 0.8522 (tm-30) REVERT: B 133 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8626 (tp30) REVERT: B 173 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8882 (mmmm) REVERT: C 54 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8545 (mm-30) REVERT: C 465 ARG cc_start: 0.9189 (ttm170) cc_final: 0.8941 (mtp-110) REVERT: D 187 GLU cc_start: 0.9471 (tt0) cc_final: 0.9263 (tm-30) REVERT: D 220 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8940 (tm-30) REVERT: D 229 MET cc_start: 0.9372 (ptm) cc_final: 0.9105 (ptt) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 0.1205 time to fit residues: 24.8795 Evaluate side-chains 128 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 130 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 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 = 0.3301 r_free = 0.3301 target = 0.069129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053137 restraints weight = 51865.715| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.17 r_work: 0.2721 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14540 Z= 0.111 Angle : 0.497 10.349 19672 Z= 0.248 Chirality : 0.038 0.143 2190 Planarity : 0.004 0.052 2566 Dihedral : 5.203 87.888 2039 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.18 % Allowed : 12.96 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.91 (0.20), residues: 1832 helix: 2.24 (0.18), residues: 910 sheet: -0.48 (0.34), residues: 228 loop : -1.30 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 402 TYR 0.011 0.001 TYR B 83 PHE 0.011 0.001 PHE D 418 TRP 0.002 0.001 TRP C 111 HIS 0.002 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00258 (14540) covalent geometry : angle 0.49687 (19672) hydrogen bonds : bond 0.02890 ( 716) hydrogen bonds : angle 3.68191 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9234 (mt) cc_final: 0.8989 (mm) REVERT: A 229 MET cc_start: 0.9242 (ptm) cc_final: 0.8391 (ptm) REVERT: A 232 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9030 (pt) REVERT: A 449 LYS cc_start: 0.8595 (tppt) cc_final: 0.8249 (tppt) REVERT: B 21 MET cc_start: 0.9049 (ttp) cc_final: 0.8664 (ttp) REVERT: B 49 GLU cc_start: 0.7839 (mp0) cc_final: 0.7633 (mp0) REVERT: B 63 GLU cc_start: 0.8972 (tt0) cc_final: 0.8526 (tm-30) REVERT: B 133 GLU cc_start: 0.8920 (tp30) cc_final: 0.8600 (tp30) REVERT: B 173 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8905 (mmmm) REVERT: C 210 GLU cc_start: 0.9083 (mp0) cc_final: 0.8668 (mp0) REVERT: C 465 ARG cc_start: 0.9193 (ttm170) cc_final: 0.8944 (mtp-110) REVERT: D 187 GLU cc_start: 0.9481 (tt0) cc_final: 0.9266 (tm-30) REVERT: D 220 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8914 (tm-30) REVERT: D 229 MET cc_start: 0.9380 (ptm) cc_final: 0.9130 (ptt) outliers start: 33 outliers final: 20 residues processed: 146 average time/residue: 0.1203 time to fit residues: 26.6022 Evaluate side-chains 133 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 247 HIS ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.051612 restraints weight = 51804.995| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.11 r_work: 0.2670 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14540 Z= 0.135 Angle : 0.519 8.301 19672 Z= 0.261 Chirality : 0.039 0.140 2190 Planarity : 0.004 0.055 2566 Dihedral : 5.296 87.775 2039 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.25 % Allowed : 12.76 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 1.03 (0.20), residues: 1832 helix: 2.30 (0.18), residues: 914 sheet: -0.35 (0.35), residues: 226 loop : -1.21 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 393 TYR 0.009 0.001 TYR A 172 PHE 0.014 0.001 PHE D 418 TRP 0.002 0.001 TRP A 111 HIS 0.003 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00316 (14540) covalent geometry : angle 0.51913 (19672) hydrogen bonds : bond 0.03194 ( 716) hydrogen bonds : angle 3.74447 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.8223 (t) cc_final: 0.7941 (t) REVERT: A 160 ILE cc_start: 0.9343 (mt) cc_final: 0.9118 (mm) REVERT: A 229 MET cc_start: 0.9364 (ptm) cc_final: 0.8427 (ptm) REVERT: A 232 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9035 (pt) REVERT: A 389 CYS cc_start: 0.7953 (m) cc_final: 0.7393 (m) REVERT: A 449 LYS cc_start: 0.8629 (tppt) cc_final: 0.8309 (tppt) REVERT: A 480 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7177 (tt) REVERT: B 21 MET cc_start: 0.9029 (ttp) cc_final: 0.8651 (ttp) REVERT: B 49 GLU cc_start: 0.7898 (mp0) cc_final: 0.7686 (mp0) REVERT: B 63 GLU cc_start: 0.9018 (tt0) cc_final: 0.8556 (tm-30) REVERT: B 133 GLU cc_start: 0.8891 (tp30) cc_final: 0.8588 (tp30) REVERT: B 142 ASP cc_start: 0.7103 (t0) cc_final: 0.6029 (t70) REVERT: B 173 LYS cc_start: 0.9214 (mmmm) cc_final: 0.9003 (mmmt) REVERT: C 210 GLU cc_start: 0.9127 (mp0) cc_final: 0.8698 (mp0) REVERT: C 449 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8213 (mmmt) REVERT: C 465 ARG cc_start: 0.9236 (ttm170) cc_final: 0.8988 (mtp-110) REVERT: D 187 GLU cc_start: 0.9489 (tt0) cc_final: 0.9256 (tm-30) REVERT: D 220 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8899 (tm-30) REVERT: D 229 MET cc_start: 0.9433 (ptm) cc_final: 0.9223 (ptt) outliers start: 34 outliers final: 22 residues processed: 140 average time/residue: 0.1268 time to fit residues: 26.5031 Evaluate side-chains 136 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 35 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN C 231 HIS ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.051682 restraints weight = 51469.231| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.10 r_work: 0.2670 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14540 Z= 0.127 Angle : 0.525 9.404 19672 Z= 0.263 Chirality : 0.039 0.141 2190 Planarity : 0.004 0.054 2566 Dihedral : 5.270 87.501 2038 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.85 % Allowed : 13.62 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 1.10 (0.20), residues: 1832 helix: 2.34 (0.18), residues: 914 sheet: -0.34 (0.35), residues: 226 loop : -1.15 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 393 TYR 0.010 0.001 TYR A 172 PHE 0.012 0.001 PHE D 418 TRP 0.002 0.001 TRP D 111 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00297 (14540) covalent geometry : angle 0.52472 (19672) hydrogen bonds : bond 0.03095 ( 716) hydrogen bonds : angle 3.72227 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.8284 (t) cc_final: 0.8004 (t) REVERT: A 160 ILE cc_start: 0.9343 (mt) cc_final: 0.9126 (mm) REVERT: A 229 MET cc_start: 0.9352 (ptm) cc_final: 0.8664 (ptm) REVERT: A 389 CYS cc_start: 0.7951 (m) cc_final: 0.7413 (m) REVERT: A 449 LYS cc_start: 0.8643 (tppt) cc_final: 0.8277 (tppt) REVERT: B 21 MET cc_start: 0.9013 (ttp) cc_final: 0.8650 (ttp) REVERT: B 49 GLU cc_start: 0.7914 (mp0) cc_final: 0.7714 (mp0) REVERT: B 63 GLU cc_start: 0.9021 (tt0) cc_final: 0.8571 (tm-30) REVERT: B 133 GLU cc_start: 0.8918 (tp30) cc_final: 0.8493 (tp30) REVERT: B 142 ASP cc_start: 0.7129 (t0) cc_final: 0.6036 (t70) REVERT: B 173 LYS cc_start: 0.9226 (mmmm) cc_final: 0.9015 (mmmt) REVERT: B 384 CYS cc_start: 0.8659 (p) cc_final: 0.8357 (p) REVERT: C 210 GLU cc_start: 0.9142 (mp0) cc_final: 0.8701 (mp0) REVERT: C 432 THR cc_start: 0.8917 (m) cc_final: 0.8617 (p) REVERT: C 465 ARG cc_start: 0.9233 (ttm170) cc_final: 0.8993 (mtp-110) REVERT: D 187 GLU cc_start: 0.9474 (tt0) cc_final: 0.9249 (tm-30) REVERT: D 220 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8889 (tm-30) outliers start: 28 outliers final: 24 residues processed: 133 average time/residue: 0.1170 time to fit residues: 23.4106 Evaluate side-chains 134 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 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 = 0.3260 r_free = 0.3260 target = 0.067434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.051593 restraints weight = 51598.306| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.12 r_work: 0.2668 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14540 Z= 0.127 Angle : 0.530 9.260 19672 Z= 0.264 Chirality : 0.039 0.292 2190 Planarity : 0.004 0.053 2566 Dihedral : 5.284 87.528 2038 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 13.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 1.17 (0.20), residues: 1832 helix: 2.37 (0.17), residues: 914 sheet: -0.33 (0.35), residues: 226 loop : -1.06 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 393 TYR 0.010 0.001 TYR A 172 PHE 0.012 0.001 PHE D 418 TRP 0.002 0.001 TRP D 111 HIS 0.002 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00296 (14540) covalent geometry : angle 0.53034 (19672) hydrogen bonds : bond 0.03098 ( 716) hydrogen bonds : angle 3.73420 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.8347 (t) cc_final: 0.8071 (t) REVERT: A 229 MET cc_start: 0.9366 (ptm) cc_final: 0.8665 (ptm) REVERT: A 232 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9005 (pt) REVERT: A 389 CYS cc_start: 0.7897 (m) cc_final: 0.7376 (m) REVERT: A 449 LYS cc_start: 0.8593 (tppt) cc_final: 0.8316 (tppt) REVERT: A 480 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (tt) REVERT: B 21 MET cc_start: 0.9057 (ttp) cc_final: 0.8692 (ttp) REVERT: B 49 GLU cc_start: 0.7884 (mp0) cc_final: 0.7678 (mp0) REVERT: B 63 GLU cc_start: 0.9012 (tt0) cc_final: 0.8562 (tm-30) REVERT: B 142 ASP cc_start: 0.7210 (t0) cc_final: 0.6095 (t70) REVERT: B 173 LYS cc_start: 0.9246 (mmmm) cc_final: 0.9038 (mmmt) REVERT: B 384 CYS cc_start: 0.8676 (p) cc_final: 0.8370 (p) REVERT: C 210 GLU cc_start: 0.9098 (mp0) cc_final: 0.8661 (mp0) REVERT: C 432 THR cc_start: 0.8917 (m) cc_final: 0.8620 (p) REVERT: C 465 ARG cc_start: 0.9214 (ttm170) cc_final: 0.8986 (mtp-110) REVERT: D 220 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8908 (tm-30) outliers start: 28 outliers final: 23 residues processed: 133 average time/residue: 0.1242 time to fit residues: 24.7643 Evaluate side-chains 136 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 153 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 130 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 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 = 0.3281 r_free = 0.3281 target = 0.068563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.052865 restraints weight = 50861.149| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.03 r_work: 0.2702 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14540 Z= 0.100 Angle : 0.522 10.334 19672 Z= 0.259 Chirality : 0.039 0.327 2190 Planarity : 0.004 0.051 2566 Dihedral : 5.253 87.735 2038 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.59 % Allowed : 14.02 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 1.17 (0.20), residues: 1832 helix: 2.38 (0.18), residues: 910 sheet: -0.45 (0.37), residues: 206 loop : -1.00 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 451 TYR 0.012 0.001 TYR B 83 PHE 0.008 0.001 PHE D 418 TRP 0.002 0.001 TRP C 111 HIS 0.002 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00229 (14540) covalent geometry : angle 0.52218 (19672) hydrogen bonds : bond 0.02836 ( 716) hydrogen bonds : angle 3.67897 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 74 SER cc_start: 0.8299 (t) cc_final: 0.8025 (t) REVERT: A 229 MET cc_start: 0.9313 (ptm) cc_final: 0.8682 (ptm) REVERT: A 389 CYS cc_start: 0.8014 (m) cc_final: 0.7622 (m) REVERT: A 449 LYS cc_start: 0.8623 (tppt) cc_final: 0.8345 (tppt) REVERT: B 21 MET cc_start: 0.9022 (ttp) cc_final: 0.8647 (ttp) REVERT: B 49 GLU cc_start: 0.7855 (mp0) cc_final: 0.7643 (mp0) REVERT: B 63 GLU cc_start: 0.9007 (tt0) cc_final: 0.8558 (tm-30) REVERT: B 142 ASP cc_start: 0.7112 (t0) cc_final: 0.6008 (t70) REVERT: B 173 LYS cc_start: 0.9216 (mmmm) cc_final: 0.9007 (mmmt) REVERT: B 384 CYS cc_start: 0.8688 (p) cc_final: 0.8355 (p) REVERT: C 210 GLU cc_start: 0.9075 (mp0) cc_final: 0.8759 (mp0) REVERT: C 432 THR cc_start: 0.8879 (m) cc_final: 0.8586 (p) REVERT: C 465 ARG cc_start: 0.9220 (ttm170) cc_final: 0.8966 (mtp-110) REVERT: D 220 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8896 (tm-30) REVERT: D 231 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8219 (t-90) outliers start: 24 outliers final: 20 residues processed: 128 average time/residue: 0.1211 time to fit residues: 23.4769 Evaluate side-chains 129 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 137 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 120 optimal weight: 0.0870 chunk 28 optimal weight: 0.3980 chunk 170 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 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 = 0.3288 r_free = 0.3288 target = 0.068710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.052932 restraints weight = 51420.687| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.10 r_work: 0.2704 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14540 Z= 0.100 Angle : 0.521 10.304 19672 Z= 0.258 Chirality : 0.039 0.322 2190 Planarity : 0.004 0.050 2566 Dihedral : 5.219 87.909 2038 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.72 % Allowed : 13.89 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 1.25 (0.20), residues: 1832 helix: 2.41 (0.18), residues: 910 sheet: -0.38 (0.37), residues: 206 loop : -0.93 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 402 TYR 0.011 0.001 TYR A 172 PHE 0.011 0.001 PHE C 193 TRP 0.002 0.001 TRP B 111 HIS 0.002 0.000 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00228 (14540) covalent geometry : angle 0.52126 (19672) hydrogen bonds : bond 0.02759 ( 716) hydrogen bonds : angle 3.64017 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.70 seconds wall clock time: 54 minutes 57.86 seconds (3297.86 seconds total)