Starting phenix.real_space_refine on Wed Mar 4 14:58:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlv_22381/03_2026/7jlv_22381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlv_22381/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jlv_22381/03_2026/7jlv_22381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlv_22381/03_2026/7jlv_22381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jlv_22381/03_2026/7jlv_22381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlv_22381/03_2026/7jlv_22381.map" } 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-5986/lib/python3.9/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: 2.66, per 1000 atoms: 0.19 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: 0.86 Conformation dependent library (CDL) restraints added in 563.9 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: 0.33 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: 1.85 Time building geometry restraints manager: 1.16 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: 7379 16.46 - 32.93: 1137 32.93 - 49.39: 340 49.39 - 65.86: 52 65.86 - 82.32: 20 Dihedral angle restraints: 8928 sinusoidal: 3820 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 8925 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: 0.03 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: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.760 Find NCS groups from input model: 0.130 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 17.005 82.321 5632 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 covalent geometry : bond 0.00418 (14612) covalent geometry : angle 0.85363 (19712) hydrogen bonds : bond 0.22277 ( 560) hydrogen bonds : angle 6.51037 ( 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 : 0.466 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1232 time to fit residues: 40.6559 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 : 0.440 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 304 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114443 restraints weight = 22356.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116791 restraints weight = 15392.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118125 restraints weight = 11128.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119017 restraints weight = 8712.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119757 restraints weight = 7140.021| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14612 Z= 0.114 Angle : 0.595 6.297 19712 Z= 0.303 Chirality : 0.042 0.152 2192 Planarity : 0.004 0.051 2464 Dihedral : 10.106 66.662 2044 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.26 % Allowed : 11.38 % Favored : 88.36 % 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: -0.99 (0.20), residues: 1740 helix: 0.55 (0.18), residues: 800 sheet: 0.54 (0.44), residues: 196 loop : -2.44 (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 A 444 TRP 0.005 0.001 TRP A 404 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00241 (14612) covalent geometry : angle 0.59525 (19712) hydrogen bonds : bond 0.03962 ( 560) hydrogen bonds : angle 4.48256 ( 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 205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 201 time to evaluate : 0.559 Fit side-chains REVERT: A 344 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7854 (tm-30) REVERT: B 344 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 344 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7856 (tm-30) REVERT: G 344 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7856 (tm-30) outliers start: 4 outliers final: 0 residues processed: 205 average time/residue: 0.1344 time to fit residues: 39.0227 Evaluate side-chains 181 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 9.9990 chunk 110 optimal weight: 0.0170 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112799 restraints weight = 22591.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114811 restraints weight = 15098.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116324 restraints weight = 11132.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117369 restraints weight = 8734.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118031 restraints weight = 7205.757| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14612 Z= 0.106 Angle : 0.542 6.122 19712 Z= 0.281 Chirality : 0.042 0.150 2192 Planarity : 0.004 0.046 2464 Dihedral : 9.464 67.225 2044 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.51 % Allowed : 14.58 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1740 helix: 0.75 (0.18), residues: 796 sheet: 0.78 (0.43), residues: 192 loop : -2.45 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 323 TYR 0.010 0.001 TYR G 546 PHE 0.008 0.001 PHE D 444 TRP 0.005 0.001 TRP G 404 HIS 0.002 0.000 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00231 (14612) covalent geometry : angle 0.54234 (19712) hydrogen bonds : bond 0.03636 ( 560) hydrogen bonds : angle 4.16137 ( 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 206 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.550 Fit side-chains REVERT: A 344 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7793 (tm-30) REVERT: B 344 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 344 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7789 (tm-30) REVERT: G 344 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7784 (tm-30) outliers start: 8 outliers final: 8 residues processed: 202 average time/residue: 0.1271 time to fit residues: 37.1721 Evaluate side-chains 186 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 268 LEU 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: 0.3980 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 144 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 169 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3478 r_free = 0.3478 target = 0.126707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114024 restraints weight = 22375.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116113 restraints weight = 15048.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117603 restraints weight = 11012.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118547 restraints weight = 8687.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119355 restraints weight = 7263.788| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14612 Z= 0.096 Angle : 0.510 6.169 19712 Z= 0.266 Chirality : 0.041 0.148 2192 Planarity : 0.004 0.048 2464 Dihedral : 8.335 63.658 2044 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.15 % Allowed : 15.60 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1740 helix: 0.79 (0.18), residues: 808 sheet: 0.87 (0.43), residues: 192 loop : -2.37 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.009 0.001 TYR D 604 PHE 0.006 0.001 PHE G 444 TRP 0.005 0.001 TRP A 585 HIS 0.003 0.000 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00201 (14612) covalent geometry : angle 0.51000 (19712) hydrogen bonds : bond 0.03069 ( 560) hydrogen bonds : angle 3.97001 ( 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 220 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.588 Fit side-chains REVERT: A 344 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 344 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 344 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7749 (tm-30) REVERT: G 344 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7740 (tm-30) outliers start: 18 outliers final: 10 residues processed: 212 average time/residue: 0.1290 time to fit residues: 39.2186 Evaluate side-chains 193 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU 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 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: 8.9990 chunk 122 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3366 r_free = 0.3366 target = 0.118714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105904 restraints weight = 22489.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107750 restraints weight = 15271.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109091 restraints weight = 11467.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109957 restraints weight = 9205.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110742 restraints weight = 7785.338| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14612 Z= 0.167 Angle : 0.594 6.166 19712 Z= 0.312 Chirality : 0.043 0.158 2192 Planarity : 0.005 0.055 2464 Dihedral : 8.567 70.868 2044 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.15 % Allowed : 16.75 % Favored : 82.10 % 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: -0.84 (0.20), residues: 1740 helix: 0.74 (0.18), residues: 796 sheet: 0.95 (0.42), residues: 200 loop : -2.55 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 323 TYR 0.013 0.002 TYR B 604 PHE 0.011 0.001 PHE D 444 TRP 0.011 0.002 TRP B 404 HIS 0.002 0.001 HIS D 463 Details of bonding type rmsd covalent geometry : bond 0.00391 (14612) covalent geometry : angle 0.59356 (19712) hydrogen bonds : bond 0.04592 ( 560) hydrogen bonds : angle 4.21458 ( 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 183 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.541 Fit side-chains REVERT: B 344 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7730 (tm-30) outliers start: 18 outliers final: 6 residues processed: 179 average time/residue: 0.1195 time to fit residues: 31.5415 Evaluate side-chains 160 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3406 r_free = 0.3406 target = 0.121554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108776 restraints weight = 22288.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110697 restraints weight = 15183.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112116 restraints weight = 11320.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113105 restraints weight = 8976.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113749 restraints weight = 7515.170| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2245 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= 0.112 Angle : 0.535 6.328 19712 Z= 0.280 Chirality : 0.041 0.147 2192 Planarity : 0.004 0.057 2464 Dihedral : 8.133 65.738 2044 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.53 % Allowed : 18.16 % Favored : 80.31 % 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: -0.70 (0.20), residues: 1740 helix: 0.80 (0.18), residues: 800 sheet: 1.10 (0.43), residues: 192 loop : -2.42 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 323 TYR 0.012 0.001 TYR A 604 PHE 0.006 0.001 PHE G 444 TRP 0.006 0.001 TRP G 585 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00247 (14612) covalent geometry : angle 0.53511 (19712) hydrogen bonds : bond 0.03547 ( 560) hydrogen bonds : angle 4.04821 ( 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 185 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.412 Fit side-chains REVERT: A 344 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 344 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7625 (tm-30) REVERT: D 344 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7633 (tm-30) REVERT: G 344 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7625 (tm-30) outliers start: 24 outliers final: 19 residues processed: 184 average time/residue: 0.1212 time to fit residues: 32.8470 Evaluate side-chains 174 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 425 ILE 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 403 VAL 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 403 VAL Chi-restraints excluded: chain D residue 425 ILE 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 403 VAL Chi-restraints excluded: chain G residue 425 ILE 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: 6.9990 chunk 162 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.120274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107388 restraints weight = 22266.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109282 restraints weight = 15143.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110684 restraints weight = 11303.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111603 restraints weight = 9041.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112351 restraints weight = 7627.554| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14612 Z= 0.123 Angle : 0.539 6.171 19712 Z= 0.284 Chirality : 0.042 0.156 2192 Planarity : 0.004 0.058 2464 Dihedral : 8.190 66.133 2044 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.30 % Allowed : 17.52 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.66 (0.20), residues: 1740 helix: 0.83 (0.18), residues: 800 sheet: 1.17 (0.43), residues: 192 loop : -2.40 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 323 TYR 0.011 0.001 TYR D 604 PHE 0.007 0.001 PHE A 444 TRP 0.007 0.001 TRP A 404 HIS 0.002 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00279 (14612) covalent geometry : angle 0.53936 (19712) hydrogen bonds : bond 0.03787 ( 560) hydrogen bonds : angle 4.04040 ( 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 207 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.553 Fit side-chains REVERT: A 344 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 344 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 344 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7581 (tm-30) REVERT: G 276 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7604 (m) REVERT: G 344 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7580 (tm-30) outliers start: 36 outliers final: 19 residues processed: 207 average time/residue: 0.1124 time to fit residues: 35.1179 Evaluate side-chains 174 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 403 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 VAL 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 D residue 403 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 425 ILE 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: 0.9980 chunk 46 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 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 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 = 0.3401 r_free = 0.3401 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108285 restraints weight = 22228.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110161 restraints weight = 15094.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111409 restraints weight = 11274.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112554 restraints weight = 9083.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113173 restraints weight = 7562.291| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14612 Z= 0.111 Angle : 0.527 6.590 19712 Z= 0.279 Chirality : 0.041 0.158 2192 Planarity : 0.004 0.059 2464 Dihedral : 8.076 64.071 2044 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.98 % Allowed : 17.33 % 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: -0.65 (0.20), residues: 1740 helix: 0.84 (0.18), residues: 800 sheet: 1.14 (0.42), residues: 192 loop : -2.40 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 323 TYR 0.011 0.001 TYR D 604 PHE 0.006 0.001 PHE A 444 TRP 0.006 0.001 TRP G 217 HIS 0.002 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00246 (14612) covalent geometry : angle 0.52710 (19712) hydrogen bonds : bond 0.03480 ( 560) hydrogen bonds : angle 4.03307 ( 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 197 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.537 Fit side-chains REVERT: B 276 CYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7524 (m) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.1080 time to fit residues: 31.7417 Evaluate side-chains 179 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 425 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 VAL 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 D residue 403 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 425 ILE 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: 0.7980 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 110 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3427 r_free = 0.3427 target = 0.122899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109935 restraints weight = 22381.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111906 restraints weight = 15037.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113335 restraints weight = 11158.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114280 restraints weight = 8847.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115058 restraints weight = 7436.398| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14612 Z= 0.099 Angle : 0.528 11.055 19712 Z= 0.274 Chirality : 0.041 0.197 2192 Planarity : 0.004 0.057 2464 Dihedral : 7.857 60.150 2044 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.79 % Allowed : 17.52 % 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: -0.59 (0.21), residues: 1740 helix: 0.90 (0.18), residues: 800 sheet: 1.09 (0.42), residues: 192 loop : -2.34 (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 0.005 0.001 PHE A 232 TRP 0.005 0.001 TRP D 217 HIS 0.002 0.000 HIS G 304 Details of bonding type rmsd covalent geometry : bond 0.00214 (14612) covalent geometry : angle 0.52849 (19712) hydrogen bonds : bond 0.03092 ( 560) hydrogen bonds : angle 3.94258 ( 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 193 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 344 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7567 (tm-30) outliers start: 28 outliers final: 21 residues processed: 193 average time/residue: 0.1148 time to fit residues: 33.3901 Evaluate side-chains 177 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 403 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 425 ILE 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 403 VAL Chi-restraints excluded: chain G residue 425 ILE 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: 0.1980 chunk 125 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3379 r_free = 0.3379 target = 0.119505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106700 restraints weight = 22357.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108562 restraints weight = 15191.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109938 restraints weight = 11345.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110896 restraints weight = 9092.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111663 restraints weight = 7629.886| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14612 Z= 0.139 Angle : 0.591 11.234 19712 Z= 0.303 Chirality : 0.043 0.182 2192 Planarity : 0.004 0.059 2464 Dihedral : 8.131 63.015 2044 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.66 % Allowed : 17.65 % 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: -0.69 (0.20), residues: 1740 helix: 0.82 (0.18), residues: 800 sheet: 1.11 (0.41), residues: 200 loop : -2.47 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 323 TYR 0.012 0.001 TYR A 546 PHE 0.008 0.001 PHE A 444 TRP 0.007 0.001 TRP B 404 HIS 0.003 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00325 (14612) covalent geometry : angle 0.59071 (19712) hydrogen bonds : bond 0.03903 ( 560) hydrogen bonds : angle 4.06654 ( 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 183 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.536 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 183 average time/residue: 0.1170 time to fit residues: 32.1584 Evaluate side-chains 173 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 403 VAL Chi-restraints excluded: chain A residue 425 ILE 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 403 VAL Chi-restraints excluded: chain B residue 425 ILE 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 403 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 425 ILE 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: 4.9990 chunk 106 optimal weight: 0.9990 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: 0.2980 chunk 94 optimal weight: 0.0170 chunk 109 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3421 r_free = 0.3421 target = 0.122435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109502 restraints weight = 22388.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111459 restraints weight = 15055.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112880 restraints weight = 11199.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113908 restraints weight = 8872.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114554 restraints weight = 7408.819| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14612 Z= 0.105 Angle : 0.550 10.242 19712 Z= 0.282 Chirality : 0.042 0.183 2192 Planarity : 0.004 0.056 2464 Dihedral : 7.877 60.329 2044 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.47 % Allowed : 17.90 % Favored : 80.63 % 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: -0.60 (0.20), residues: 1740 helix: 0.85 (0.18), residues: 804 sheet: 1.12 (0.42), residues: 192 loop : -2.32 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 323 TYR 0.011 0.001 TYR D 604 PHE 0.006 0.001 PHE A 232 TRP 0.006 0.001 TRP B 217 HIS 0.002 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00229 (14612) covalent geometry : angle 0.55039 (19712) hydrogen bonds : bond 0.03180 ( 560) hydrogen bonds : angle 4.02370 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.82 seconds wall clock time: 34 minutes 19.60 seconds (2059.60 seconds total)