Starting phenix.real_space_refine on Thu Sep 26 23:53:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/09_2024/7jlv_22381.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/09_2024/7jlv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/09_2024/7jlv_22381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/09_2024/7jlv_22381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/09_2024/7jlv_22381.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/09_2024/7jlv_22381.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 9.01, per 1000 atoms: 0.63 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: 4.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.49 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: 4.12 Time building geometry restraints manager: 4.70 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: 0.00 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: 7.040 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: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 33.820 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- 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= 0.263 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 TRP 0.009 0.001 TRP B 582 HIS 0.003 0.001 HIS G 304 PHE 0.019 0.001 PHE D 357 TYR 0.027 0.003 TYR B 397 ARG 0.005 0.001 ARG B 289 *********************** 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 fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.873 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2893 time to fit residues: 94.7473 Evaluate side-chains 187 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14612 Z= 0.165 Angle : 0.599 6.286 19712 Z= 0.306 Chirality : 0.042 0.162 2192 Planarity : 0.004 0.053 2464 Dihedral : 10.083 67.942 2044 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.26 % Allowed : 11.06 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1740 helix: 0.57 (0.18), residues: 796 sheet: 0.58 (0.44), residues: 196 loop : -2.47 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 404 HIS 0.003 0.001 HIS A 304 PHE 0.008 0.001 PHE D 444 TYR 0.009 0.001 TYR G 546 ARG 0.003 0.000 ARG G 506 *********************** 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 197 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.741 Fit side-chains REVERT: A 344 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 344 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 344 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7834 (tm-30) REVERT: G 344 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7832 (tm-30) outliers start: 4 outliers final: 0 residues processed: 197 average time/residue: 0.3147 time to fit residues: 86.6451 Evaluate side-chains 175 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14612 Z= 0.197 Angle : 0.578 6.261 19712 Z= 0.300 Chirality : 0.043 0.161 2192 Planarity : 0.004 0.050 2464 Dihedral : 9.791 73.727 2044 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.58 % Allowed : 14.26 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1740 helix: 0.68 (0.18), residues: 792 sheet: 0.80 (0.43), residues: 196 loop : -2.54 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 404 HIS 0.002 0.001 HIS G 304 PHE 0.010 0.001 PHE G 444 TYR 0.012 0.001 TYR G 546 ARG 0.004 0.000 ARG A 323 *********************** 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 200 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 1.698 Fit side-chains REVERT: A 344 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 344 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 344 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7783 (tm-30) REVERT: G 344 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7786 (tm-30) outliers start: 9 outliers final: 4 residues processed: 195 average time/residue: 0.3093 time to fit residues: 86.4512 Evaluate side-chains 161 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 G residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14612 Z= 0.141 Angle : 0.531 6.329 19712 Z= 0.277 Chirality : 0.041 0.150 2192 Planarity : 0.004 0.051 2464 Dihedral : 8.736 70.391 2044 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.90 % Allowed : 16.62 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1740 helix: 0.77 (0.18), residues: 800 sheet: 0.98 (0.43), residues: 192 loop : -2.44 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 585 HIS 0.003 0.000 HIS B 304 PHE 0.006 0.001 PHE G 444 TYR 0.011 0.001 TYR D 604 ARG 0.003 0.000 ARG A 323 *********************** 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 192 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.694 Fit side-chains REVERT: A 344 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 484 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 344 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7741 (tm-30) REVERT: D 344 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7748 (tm-30) REVERT: G 344 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7749 (tm-30) REVERT: G 484 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (mt) outliers start: 14 outliers final: 4 residues processed: 189 average time/residue: 0.2676 time to fit residues: 74.1452 Evaluate side-chains 161 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 D residue 268 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2046 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= 0.163 Angle : 0.534 6.273 19712 Z= 0.280 Chirality : 0.042 0.175 2192 Planarity : 0.004 0.054 2464 Dihedral : 8.230 71.740 2044 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.09 % Allowed : 17.26 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1740 helix: 0.81 (0.18), residues: 800 sheet: 1.06 (0.43), residues: 192 loop : -2.42 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 585 HIS 0.003 0.001 HIS G 304 PHE 0.007 0.001 PHE B 444 TYR 0.011 0.001 TYR D 604 ARG 0.004 0.000 ARG G 323 *********************** 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 193 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.772 Fit side-chains REVERT: A 344 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 484 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 344 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 344 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7683 (tm-30) REVERT: G 344 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7685 (tm-30) REVERT: G 484 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8341 (mt) outliers start: 17 outliers final: 11 residues processed: 193 average time/residue: 0.2892 time to fit residues: 82.1276 Evaluate side-chains 165 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 484 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 588 TYR 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 484 ILE 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 55 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 160 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14612 Z= 0.128 Angle : 0.515 6.196 19712 Z= 0.268 Chirality : 0.041 0.153 2192 Planarity : 0.004 0.053 2464 Dihedral : 7.892 68.572 2044 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.53 % Allowed : 17.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1740 helix: 0.88 (0.18), residues: 804 sheet: 1.04 (0.42), residues: 192 loop : -2.35 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 585 HIS 0.003 0.000 HIS B 304 PHE 0.005 0.001 PHE A 232 TYR 0.009 0.001 TYR B 604 ARG 0.003 0.000 ARG D 323 *********************** 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 201 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.763 Fit side-chains REVERT: A 344 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 344 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7631 (tm-30) REVERT: D 344 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7632 (tm-30) REVERT: G 344 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7617 (tm-30) outliers start: 24 outliers final: 11 residues processed: 197 average time/residue: 0.2594 time to fit residues: 76.1929 Evaluate side-chains 168 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 588 TYR 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 18 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14612 Z= 0.151 Angle : 0.525 6.009 19712 Z= 0.273 Chirality : 0.041 0.168 2192 Planarity : 0.004 0.054 2464 Dihedral : 7.933 70.393 2044 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.66 % Allowed : 17.97 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1740 helix: 0.94 (0.18), residues: 800 sheet: 1.09 (0.42), residues: 192 loop : -2.35 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 582 HIS 0.003 0.001 HIS A 304 PHE 0.006 0.001 PHE B 444 TYR 0.010 0.001 TYR A 604 ARG 0.004 0.000 ARG B 323 *********************** 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 201 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.735 Fit side-chains REVERT: A 344 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 344 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 344 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7615 (tm-30) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.2520 time to fit residues: 75.4380 Evaluate side-chains 175 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 588 TYR 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 588 TYR 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 588 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14612 Z= 0.243 Angle : 0.599 6.325 19712 Z= 0.312 Chirality : 0.044 0.157 2192 Planarity : 0.005 0.061 2464 Dihedral : 8.618 82.066 2044 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.92 % Allowed : 17.97 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1740 helix: 0.74 (0.18), residues: 800 sheet: 1.09 (0.42), residues: 200 loop : -2.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 582 HIS 0.003 0.001 HIS D 337 PHE 0.010 0.001 PHE B 444 TYR 0.012 0.001 TYR A 546 ARG 0.006 0.000 ARG G 323 *********************** 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 182 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.866 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 182 average time/residue: 0.2577 time to fit residues: 69.4358 Evaluate side-chains 158 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 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 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 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 588 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14612 Z= 0.186 Angle : 0.556 7.021 19712 Z= 0.290 Chirality : 0.042 0.183 2192 Planarity : 0.004 0.061 2464 Dihedral : 8.367 82.580 2044 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.53 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1740 helix: 0.79 (0.18), residues: 800 sheet: 1.08 (0.41), residues: 200 loop : -2.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.002 0.001 HIS D 304 PHE 0.007 0.001 PHE B 444 TYR 0.012 0.001 TYR B 604 ARG 0.005 0.000 ARG D 323 *********************** 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 183 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.738 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 183 average time/residue: 0.2660 time to fit residues: 72.7661 Evaluate side-chains 164 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 425 ILE 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 588 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU 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 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 171 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14612 Z= 0.156 Angle : 0.543 6.999 19712 Z= 0.282 Chirality : 0.042 0.180 2192 Planarity : 0.004 0.057 2464 Dihedral : 8.153 83.602 2044 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.09 % Allowed : 18.41 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1740 helix: 0.84 (0.18), residues: 800 sheet: 1.07 (0.41), residues: 200 loop : -2.49 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.002 0.000 HIS D 304 PHE 0.006 0.001 PHE D 444 TYR 0.012 0.001 TYR D 546 ARG 0.004 0.000 ARG B 323 ********************** 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 180 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.727 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 180 average time/residue: 0.2797 time to fit residues: 75.2298 Evaluate side-chains 176 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 425 ILE 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 588 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU 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 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.116978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104124 restraints weight = 22399.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105942 restraints weight = 15234.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107245 restraints weight = 11454.413| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14612 Z= 0.239 Angle : 0.590 6.394 19712 Z= 0.308 Chirality : 0.044 0.183 2192 Planarity : 0.005 0.061 2464 Dihedral : 8.643 86.232 2044 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.21 % Allowed : 18.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1740 helix: 0.70 (0.18), residues: 800 sheet: 1.18 (0.42), residues: 200 loop : -2.61 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 404 HIS 0.002 0.001 HIS D 337 PHE 0.009 0.001 PHE D 444 TYR 0.012 0.001 TYR G 546 ARG 0.006 0.000 ARG G 323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.23 seconds wall clock time: 52 minutes 39.94 seconds (3159.94 seconds total)