Starting phenix.real_space_refine on Fri Jul 3 13:38:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlv_22381/07_2026/7jlv_22381.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 76 5.16 5 C 9176 2.51 5 N 2396 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 208 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14336 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3552 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 425} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, D, G Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14336 At special positions: 0 Unit cell: (122.957, 122.957, 98.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 12 15.00 Mg 4 11.99 O 2672 8.00 N 2396 7.00 C 9176 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: 1.13 Conformation dependent library (CDL) restraints added in 574.6 milliseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 50.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.575A pdb=" N ILE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.558A pdb=" N MET A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.122A pdb=" N LEU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.569A pdb=" N HIS A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 362 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.629A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.782A pdb=" N TRP A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.657A pdb=" N MET A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'A' and resid 463 through 474 removed outlier: 4.074A pdb=" N LYS A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.505A pdb=" N LYS A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.554A pdb=" N ALA A 525 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.646A pdb=" N TYR A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.612A pdb=" N LYS A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.574A pdb=" N ILE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.558A pdb=" N MET B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.122A pdb=" N LEU B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.570A pdb=" N HIS B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 362 Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.630A pdb=" N LEU B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 414 removed outlier: 3.781A pdb=" N TRP B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.657A pdb=" N MET B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 449 through 460 Processing helix chain 'B' and resid 463 through 474 removed outlier: 4.073A pdb=" N LYS B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.506A pdb=" N LYS B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.554A pdb=" N ALA B 525 " --> pdb=" O ARG B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.646A pdb=" N TYR B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 552 removed outlier: 3.612A pdb=" N LYS B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.575A pdb=" N ILE D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 236 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 278 through 291 removed outlier: 3.558A pdb=" N MET D 282 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 291 " --> pdb=" O LYS D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 4.122A pdb=" N LEU D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 337 removed outlier: 3.570A pdb=" N HIS D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 362 Processing helix chain 'D' and resid 371 through 383 Processing helix chain 'D' and resid 385 through 396 removed outlier: 3.629A pdb=" N LEU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 414 removed outlier: 3.781A pdb=" N TRP D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D 406 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.657A pdb=" N MET D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 444 Processing helix chain 'D' and resid 449 through 460 Processing helix chain 'D' and resid 463 through 474 removed outlier: 4.074A pdb=" N LYS D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 500 Processing helix chain 'D' and resid 509 through 516 removed outlier: 3.506A pdb=" N LYS D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 526 removed outlier: 3.554A pdb=" N ALA D 525 " --> pdb=" O ARG D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.646A pdb=" N TYR D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 552 removed outlier: 3.612A pdb=" N LYS D 552 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.575A pdb=" N ILE G 197 " --> pdb=" O ILE G 193 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 204 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 236 Processing helix chain 'G' and resid 247 through 255 Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 278 through 291 removed outlier: 3.558A pdb=" N MET G 282 " --> pdb=" O ASP G 278 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS G 291 " --> pdb=" O LYS G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 removed outlier: 4.122A pdb=" N LEU G 308 " --> pdb=" O HIS G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 337 removed outlier: 3.569A pdb=" N HIS G 337 " --> pdb=" O LEU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 362 Processing helix chain 'G' and resid 371 through 383 Processing helix chain 'G' and resid 385 through 396 removed outlier: 3.630A pdb=" N LEU G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 414 removed outlier: 3.783A pdb=" N TRP G 404 " --> pdb=" O ASP G 400 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE G 405 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER G 406 " --> pdb=" O ASP G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 428 removed outlier: 3.656A pdb=" N MET G 420 " --> pdb=" O GLU G 416 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR G 422 " --> pdb=" O GLU G 418 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER G 426 " --> pdb=" O THR G 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 449 through 460 Processing helix chain 'G' and resid 463 through 474 removed outlier: 4.074A pdb=" N LYS G 469 " --> pdb=" O VAL G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 500 Processing helix chain 'G' and resid 509 through 516 removed outlier: 3.506A pdb=" N LYS G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 526 removed outlier: 3.553A pdb=" N ALA G 525 " --> pdb=" O ARG G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 546 removed outlier: 3.647A pdb=" N TYR G 546 " --> pdb=" O LEU G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 552 removed outlier: 3.612A pdb=" N LYS G 552 " --> pdb=" O ALA G 548 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 244 removed outlier: 6.302A pdb=" N VAL A 295 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 325 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 297 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR A 327 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 299 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 341 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.611A pdb=" N THR A 606 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A 585 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 244 removed outlier: 6.302A pdb=" N VAL B 295 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL B 325 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 297 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR B 327 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 299 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 341 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.611A pdb=" N THR B 606 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP B 585 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 241 through 244 removed outlier: 6.302A pdb=" N VAL D 295 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL D 325 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL D 297 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR D 327 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU D 299 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 341 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 529 through 531 removed outlier: 3.611A pdb=" N THR D 606 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP D 585 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 241 through 244 removed outlier: 6.302A pdb=" N VAL G 295 " --> pdb=" O ARG G 323 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL G 325 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G 297 " --> pdb=" O VAL G 325 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR G 327 " --> pdb=" O VAL G 297 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 299 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU G 341 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 529 through 531 removed outlier: 3.612A pdb=" N THR G 606 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP G 585 " --> pdb=" O THR G 606 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.54 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: 4588 1.34 - 1.46: 2872 1.46 - 1.58: 7004 1.58 - 1.69: 20 1.69 - 1.81: 128 Bond restraints: 14612 Sorted by residual: bond pdb=" C4 ATP A1401 " pdb=" C5 ATP A1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.64e+01 bond pdb=" C4 ATP D1401 " pdb=" C5 ATP D1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.64e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP G1401 " pdb=" C5 ATP G1401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C5 ATP G1401 " pdb=" C6 ATP G1401 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 4.99e+01 ... (remaining 14607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 19549 3.63 - 7.26: 127 7.26 - 10.89: 28 10.89 - 14.53: 0 14.53 - 18.16: 8 Bond angle restraints: 19712 Sorted by residual: angle pdb=" PB ATP A1401 " pdb=" O3B ATP A1401 " pdb=" PG ATP A1401 " ideal model delta sigma weight residual 139.87 121.71 18.16 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP G1401 " pdb=" O3B ATP G1401 " pdb=" PG ATP G1401 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP B1401 " pdb=" O3A ATP B1401 " pdb=" PB ATP B1401 " ideal model delta sigma weight residual 136.83 121.87 14.96 1.00e+00 1.00e+00 2.24e+02 ... (remaining 19707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 7323 16.46 - 32.93: 1113 32.93 - 49.39: 300 49.39 - 65.86: 52 65.86 - 82.32: 16 Dihedral angle restraints: 8804 sinusoidal: 3696 harmonic: 5108 Sorted by residual: dihedral pdb=" N ARG D 205 " pdb=" C ARG D 205 " pdb=" CA ARG D 205 " pdb=" CB ARG D 205 " ideal model delta harmonic sigma weight residual 122.80 131.53 -8.73 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" N ARG A 205 " pdb=" C ARG A 205 " pdb=" CA ARG A 205 " pdb=" CB ARG A 205 " ideal model delta harmonic sigma weight residual 122.80 131.52 -8.72 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" N ARG G 205 " pdb=" C ARG G 205 " pdb=" CA ARG G 205 " pdb=" CB ARG G 205 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 8801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1866 0.064 - 0.129: 308 0.129 - 0.193: 6 0.193 - 0.257: 4 0.257 - 0.321: 8 Chirality restraints: 2192 Sorted by residual: chirality pdb=" CA MET B 206 " pdb=" N MET B 206 " pdb=" C MET B 206 " pdb=" CB MET B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA MET D 206 " pdb=" N MET D 206 " pdb=" C MET D 206 " pdb=" CB MET D 206 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA MET G 206 " pdb=" N MET G 206 " pdb=" C MET G 206 " pdb=" CB MET G 206 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2189 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 414 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 415 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 414 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO D 415 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 414 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 415 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 415 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 415 " 0.036 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 152 2.62 - 3.19: 12592 3.19 - 3.76: 20408 3.76 - 4.33: 27821 4.33 - 4.90: 47784 Nonbonded interactions: 108757 Sorted by model distance: nonbonded pdb=" O3B ATP D1401 " pdb="MG MG D1402 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP G1401 " pdb="MG MG G1402 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP B1401 " pdb="MG MG B1402 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP A1401 " pdb="MG MG A1402 " model vdw 2.051 2.170 nonbonded pdb=" O2B ATP G1401 " pdb="MG MG G1402 " model vdw 2.056 2.170 ... (remaining 108752 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.210 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 0.082 14612 Z= 0.291 Angle : 0.854 18.157 19712 Z= 0.565 Chirality : 0.048 0.321 2192 Planarity : 0.004 0.065 2464 Dihedral : 16.609 82.321 5508 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1740 helix: 0.96 (0.19), residues: 712 sheet: 0.37 (0.42), residues: 204 loop : -2.40 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 289 TYR 0.027 0.003 TYR B 397 PHE 0.019 0.001 PHE D 357 TRP 0.009 0.001 TRP B 582 HIS 0.003 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.29 (14612) covalent geometry : angle 0.85363 / 0.57 (19712) hydrogen bonds : bond 0.22277 / 14.44 ( 560) hydrogen bonds : angle 6.51037 / 4.52 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.610 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1272 time to fit residues: 42.3008 Evaluate side-chains 187 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS G 304 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114944 restraints weight = 22346.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117159 restraints weight = 14743.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118854 restraints weight = 10088.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119432 restraints weight = 7762.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120216 restraints weight = 6582.530| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14612 Z= 0.113 Angle : 0.595 6.246 19712 Z= 0.303 Chirality : 0.042 0.158 2192 Planarity : 0.004 0.053 2464 Dihedral : 5.048 44.414 1920 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.26 % Allowed : 11.25 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1740 helix: 0.52 (0.18), residues: 800 sheet: 0.54 (0.44), residues: 196 loop : -2.45 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 506 TYR 0.009 0.001 TYR G 546 PHE 0.008 0.001 PHE D 444 TRP 0.005 0.001 TRP A 404 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14612) covalent geometry : angle 0.59496 / 0.30 (19712) hydrogen bonds : bond 0.04011 / 2.64 ( 560) hydrogen bonds : angle 4.50927 / 3.13 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 0.535 Fit side-chains REVERT: A 344 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 344 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 344 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7851 (tm-30) REVERT: G 344 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7848 (tm-30) outliers start: 4 outliers final: 0 residues processed: 202 average time/residue: 0.1300 time to fit residues: 37.2435 Evaluate side-chains 179 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 60 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114275 restraints weight = 22477.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116787 restraints weight = 15625.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118124 restraints weight = 10992.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119034 restraints weight = 8609.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120082 restraints weight = 7043.607| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14612 Z= 0.101 Angle : 0.534 6.121 19712 Z= 0.275 Chirality : 0.041 0.149 2192 Planarity : 0.004 0.045 2464 Dihedral : 4.693 40.538 1920 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.45 % Allowed : 14.00 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.20), residues: 1740 helix: 0.75 (0.18), residues: 796 sheet: 0.64 (0.43), residues: 196 loop : -2.47 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 506 TYR 0.009 0.001 TYR G 546 PHE 0.007 0.001 PHE D 444 TRP 0.004 0.001 TRP B 585 HIS 0.002 0.000 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (14612) covalent geometry : angle 0.53400 / 0.28 (19712) hydrogen bonds : bond 0.03402 / 2.23 ( 560) hydrogen bonds : angle 4.14308 / 2.88 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.572 Fit side-chains REVERT: A 344 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 344 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 344 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7784 (tm-30) REVERT: G 344 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7790 (tm-30) outliers start: 7 outliers final: 7 residues processed: 212 average time/residue: 0.1356 time to fit residues: 41.2740 Evaluate side-chains 188 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 363 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109449 restraints weight = 22528.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111425 restraints weight = 15286.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112761 restraints weight = 11384.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113830 restraints weight = 9073.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114489 restraints weight = 7545.550| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14612 Z= 0.127 Angle : 0.551 6.190 19712 Z= 0.287 Chirality : 0.042 0.153 2192 Planarity : 0.004 0.050 2464 Dihedral : 4.789 39.500 1920 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.21 % Allowed : 16.56 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1740 helix: 0.78 (0.18), residues: 800 sheet: 0.94 (0.43), residues: 192 loop : -2.48 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.011 0.001 TYR G 546 PHE 0.009 0.001 PHE B 444 TRP 0.008 0.001 TRP A 404 HIS 0.003 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14612) covalent geometry : angle 0.55146 / 0.29 (19712) hydrogen bonds : bond 0.03922 / 2.59 ( 560) hydrogen bonds : angle 4.08472 / 2.83 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.555 Fit side-chains REVERT: A 344 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 484 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B 344 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 484 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8349 (mt) REVERT: D 344 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 484 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8329 (mt) REVERT: G 344 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7753 (tm-30) outliers start: 19 outliers final: 7 residues processed: 197 average time/residue: 0.1218 time to fit residues: 34.5898 Evaluate side-chains 170 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105341 restraints weight = 22616.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107168 restraints weight = 15415.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108583 restraints weight = 11575.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109506 restraints weight = 9197.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110107 restraints weight = 7770.120| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14612 Z= 0.165 Angle : 0.602 7.127 19712 Z= 0.313 Chirality : 0.044 0.190 2192 Planarity : 0.005 0.058 2464 Dihedral : 5.204 43.638 1920 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.83 % Allowed : 17.84 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1740 helix: 0.69 (0.18), residues: 796 sheet: 0.97 (0.42), residues: 200 loop : -2.65 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 323 TYR 0.014 0.002 TYR B 604 PHE 0.011 0.001 PHE A 444 TRP 0.010 0.002 TRP A 404 HIS 0.002 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14612) covalent geometry : angle 0.60169 / 0.31 (19712) hydrogen bonds : bond 0.04569 / 3.03 ( 560) hydrogen bonds : angle 4.22878 / 2.93 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.564 Fit side-chains REVERT: A 484 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 484 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8335 (mt) REVERT: D 484 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8399 (mt) outliers start: 13 outliers final: 5 residues processed: 165 average time/residue: 0.1094 time to fit residues: 26.9413 Evaluate side-chains 150 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 40 optimal weight: 0.0010 chunk 120 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108217 restraints weight = 22282.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110145 restraints weight = 15244.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111576 restraints weight = 11383.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112610 restraints weight = 8994.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113333 restraints weight = 7463.628| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14612 Z= 0.107 Angle : 0.535 6.396 19712 Z= 0.278 Chirality : 0.042 0.156 2192 Planarity : 0.004 0.058 2464 Dihedral : 4.983 43.026 1920 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.85 % Allowed : 17.39 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1740 helix: 0.78 (0.18), residues: 800 sheet: 1.08 (0.43), residues: 192 loop : -2.45 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 323 TYR 0.012 0.001 TYR B 604 PHE 0.006 0.001 PHE B 357 TRP 0.006 0.001 TRP A 585 HIS 0.002 0.000 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14612) covalent geometry : angle 0.53548 / 0.28 (19712) hydrogen bonds : bond 0.03511 / 2.32 ( 560) hydrogen bonds : angle 4.05347 / 2.81 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.475 Fit side-chains REVERT: A 344 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 344 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7634 (tm-30) outliers start: 29 outliers final: 11 residues processed: 195 average time/residue: 0.1009 time to fit residues: 29.9222 Evaluate side-chains 168 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105441 restraints weight = 22488.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107340 restraints weight = 15442.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108697 restraints weight = 11540.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109578 restraints weight = 9251.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110333 restraints weight = 7825.198| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14612 Z= 0.143 Angle : 0.567 11.378 19712 Z= 0.295 Chirality : 0.043 0.158 2192 Planarity : 0.005 0.061 2464 Dihedral : 5.066 43.035 1920 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.34 % Allowed : 17.71 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1740 helix: 0.77 (0.18), residues: 800 sheet: 1.01 (0.42), residues: 200 loop : -2.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 323 TYR 0.012 0.001 TYR B 604 PHE 0.009 0.001 PHE G 444 TRP 0.007 0.001 TRP D 404 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14612) covalent geometry : angle 0.56713 / 0.29 (19712) hydrogen bonds : bond 0.04114 / 2.72 ( 560) hydrogen bonds : angle 4.13524 / 2.87 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.584 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 167 average time/residue: 0.1171 time to fit residues: 29.1860 Evaluate side-chains 156 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 160 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107798 restraints weight = 22342.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109689 restraints weight = 15131.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111077 restraints weight = 11368.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111996 restraints weight = 9123.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112736 restraints weight = 7699.851| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14612 Z= 0.106 Angle : 0.530 9.587 19712 Z= 0.275 Chirality : 0.042 0.167 2192 Planarity : 0.004 0.060 2464 Dihedral : 4.916 42.422 1920 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.98 % Allowed : 17.14 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1740 helix: 0.88 (0.18), residues: 800 sheet: 1.05 (0.42), residues: 192 loop : -2.41 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.011 0.001 TYR D 604 PHE 0.006 0.001 PHE G 444 TRP 0.006 0.001 TRP G 217 HIS 0.002 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14612) covalent geometry : angle 0.52962 / 0.27 (19712) hydrogen bonds : bond 0.03441 / 2.27 ( 560) hydrogen bonds : angle 4.01578 / 2.78 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 344 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7642 (tm-30) outliers start: 31 outliers final: 17 residues processed: 194 average time/residue: 0.1159 time to fit residues: 33.8862 Evaluate side-chains 165 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 126 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106405 restraints weight = 22640.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108176 restraints weight = 15290.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109613 restraints weight = 11555.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110553 restraints weight = 9226.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111293 restraints weight = 7770.142| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14612 Z= 0.130 Angle : 0.578 11.487 19712 Z= 0.295 Chirality : 0.042 0.170 2192 Planarity : 0.004 0.063 2464 Dihedral : 4.959 41.912 1920 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.34 % Allowed : 18.22 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1740 helix: 0.81 (0.18), residues: 800 sheet: 1.01 (0.41), residues: 200 loop : -2.50 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 323 TYR 0.012 0.001 TYR B 546 PHE 0.007 0.001 PHE G 444 TRP 0.007 0.001 TRP A 582 HIS 0.002 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14612) covalent geometry : angle 0.57783 / 0.30 (19712) hydrogen bonds : bond 0.03809 / 2.51 ( 560) hydrogen bonds : angle 4.07609 / 2.82 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 168 average time/residue: 0.1009 time to fit residues: 25.5756 Evaluate side-chains 164 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107341 restraints weight = 22293.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109190 restraints weight = 15046.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110486 restraints weight = 11278.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111502 restraints weight = 9036.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112158 restraints weight = 7553.449| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14612 Z= 0.114 Angle : 0.546 10.359 19712 Z= 0.281 Chirality : 0.042 0.174 2192 Planarity : 0.004 0.059 2464 Dihedral : 4.921 41.729 1920 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.28 % Allowed : 17.77 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1740 helix: 0.80 (0.18), residues: 804 sheet: 0.99 (0.41), residues: 200 loop : -2.49 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 323 TYR 0.012 0.001 TYR B 546 PHE 0.006 0.001 PHE G 444 TRP 0.006 0.001 TRP B 217 HIS 0.002 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (14612) covalent geometry : angle 0.54644 / 0.28 (19712) hydrogen bonds : bond 0.03514 / 2.31 ( 560) hydrogen bonds : angle 4.04779 / 2.80 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 170 average time/residue: 0.1064 time to fit residues: 27.2083 Evaluate side-chains 163 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 chunk 109 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS B 304 HIS D 304 HIS G 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107410 restraints weight = 22502.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109330 restraints weight = 15114.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110737 restraints weight = 11243.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111787 restraints weight = 8909.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112433 restraints weight = 7438.072| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14612 Z= 0.116 Angle : 0.561 10.107 19712 Z= 0.288 Chirality : 0.042 0.171 2192 Planarity : 0.004 0.057 2464 Dihedral : 4.906 41.591 1920 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.41 % Allowed : 17.90 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1740 helix: 0.79 (0.18), residues: 804 sheet: 1.04 (0.41), residues: 200 loop : -2.49 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.012 0.001 TYR D 546 PHE 0.006 0.001 PHE G 444 TRP 0.006 0.001 TRP B 217 HIS 0.002 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14612) covalent geometry : angle 0.56136 / 0.29 (19712) hydrogen bonds : bond 0.03519 / 2.31 ( 560) hydrogen bonds : angle 4.04777 / 2.80 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.04 seconds wall clock time: 35 minutes 4.03 seconds (2104.03 seconds total)